- ChimeraX-users - RBVI Mailing Lists

The ChimeraX-Modeller interface
by Ralph Loring 18 Feb '22

18 Feb '22

Hi, The intracellular domain (ICD) of Alpha7 nicotinic receptors, like almost all eukaryotic Cys-loop receptors, is not resolved using X-ray crystallography or cryo-EM. Last week the PDB for an ensemble of NMR ICD structures for the receptor was released (PDB 7RPM). I've been unsuccessfully trying to use ChimeraX and Modeller to make a model of a subunit that includes the ICD. The 7RPM models include all 4 transmembrane domains and the ICD (but lacks the extracellular domain), so there is considerable overlap with the 7KOO PDB fo a7. I started by deleting all but one of the identical subunits in the 7KOO pdb and loaded one of the 7RPM models and tried to use Modeller to make a construct that includes both the extracellular domain and the ICD. Unfortunately, even though both 7KOO and the single 7RPM are in the sequence alignments window, the ChimeraX-Modeller combination ignores the structure that is not chosen as the target (e.g. if 7RPM is the target, there is no extracellular domain, but if 7KOO is the target, there is either no ICD or the ICD that is shown bears no relevance to the structure in 7RPM). I can align the two structures well with a low RMSD using Matchmaker because of the TMDs overlapping. I just want to fill in the missing parts. Is there a special trick to get Modeller to fill in the missing parts using ChimeraX as the interface? I'm not that experienced using Modeller. Thanks, Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu

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surfvalues.py
by 始夏谨柘 18 Feb '22

18 Feb '22

      Hello,          This python script was downloaded on UCSF CHIMERA page (https://www.rbvi.ucsf.edu/trac/chimera/attachment/wiki/Scripts/surfvalues.p…) and running it on UCSF CHIMERA X will cause an error. UCSF CHIMERA X (https://rbvi.github.io/chimerax-recipes/) has not found the corresponding script. If I still want to achieve the function of this script (surfvalues.py) , what should I do? I tried that at UCSF CHIMERA, but the volume of the protein is too large for it. Best Wishes,                                                                                                  FAYE

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System Requirements
by Niver, Terry 17 Feb '22

17 Feb '22

Hello, I am attempting to assist a researcher here at the University of Rochester configure a new laptop on which he wants to run ChimeraX. I was trying to locate the system requirements on the website but didn’t have any luck. Would someone be able to send me a list? Thanks, Terry Terry Niver Manager, Research and Academic Information Technology Technical Support University of Rochester School of Medicine and Dentistry E-mail: terry_niver(a)urmc.rochester.edu<mailto:terry_niver@urmc.rochester.edu> Phone: 585-276-5538

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fine tuning depthcue
by vincent Chaptal 17 Feb '22

17 Feb '22

Hi, I've been playing around a lot with depthcue-ing but I can't get it to do quite what I would like. I want to display a protein structure, with a focus on one zone and a "heavy" depthcue to have a strong "fog" hiding much of the background (without deleting the residues in the back). my script includes: lighting full #(sometimes I use soft too) lighting shadows true intensity 0.3 lighting qualityOfShadows finer lighting depthcue true depthCueStart 0.1 depthCueEnd 1.0 First, I have selected one residue and setting the rotation around it by using "cofr sel" My max depthcue is with "depthCueStart 0.1 depthCueEnd 1.0". I've tried to change these numbers in many different ways, including negative or very large numbers) but I can't get it to be thicker. Could you help me please. I missed the meaning of these values, so I'm blind on their use. Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Re: [chimerax-users] VR Support
by Jessie Lopez 16 Feb '22

16 Feb '22

I am writing an article promoting the use of VR for modelling. I use an HTC Vive to access ChimeraX VR, but I have heard rumours it will be discontinued soon. The Samsung Odyssey is already discontinued. With Meta dominating the VR headset market, many companies are bailing out. Do you have any recommendations about which headsets should scientists invest in if they want to use ChimeraX? Thank you! -. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. . ||*\*|||*\* /|||*\*|||*\* /|||*\*|||*\* /|||*\*|||*\* /|||*\*|||*\* /|||*\*|||*\* /| |/ *\*|||*\*|||/ *\*|||*\*|||/ *\*|||*\*|||/ *\*|||*\*|||/ *\*|||*\*|||/ *\*|||*\*|| ~ `-~ `-` `-~ `-` `-~ `-~ `-~ `-` `-~ `-` `-~ `- *Jessie MNG Lopez Suzuki* PhD Candidate, Molecular, Cell and Developmental Biology *Zahler Laboratory* The Center for Molecular Biology of RNA University of California, Santa Cruz Sinsheimer 419 (831) 459-5127 *jlopez99(a)ucsc.edu <jlopez99(a)ucsc.edu>* (they, she or he pronouns)

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Re: [chimerax-users] Error reported by AlphaFold
by Tom Goddard 16 Feb '22

16 Feb '22

Hi Juntao, Yes, ChimeraX AlphaFold on Google Colab only handles about 1000 amino acids before running out of memory on the 5 year old GPUs (e.g. P100, K80, T4) with 16 Gbytes of GPU memory that they provide. This is a limitation of AlphaFold. Your 1500 amino acids would run fine on an Nvidia RTX 3090 GPU which has 24 Gbytes, or on higher-end GPUs like an Nvidia A40 with 48 Gbytes. These sequence size limits are a significant limitation of AlphaFold. Here is a web page I made showing AlphaFold runs that failed and succeeded and the largest sequences that worked in these tests on Colab was ~1100 residues, on an RTX 3090 it managed 2100 residues and on an A40 it got up to 3700 residues. https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html Tom > On Feb 16, 2022, at 6:56 AM, Juntao Yu <juntao_yu(a)g.harvard.edu> wrote: > > Hi Tom, > > Thank you for your email. I checked the log and realized the failure was indeed because of out of memory on Google Colab. The protein complex is about 1500 amino acids large so probably that is the reason. It’s good to know that it might take lots of memory for alphaFold to calculate large complexes. I will try to run the prediction on our clusters or lab computers with GPU instead then. Thank you. > > Best, > Juntao

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alphafold block
by Roberto Marabini 15 Feb '22

15 Feb '22

Hi, I would like to write a script that executes "alphafold predict SEQUENCE" and then postprocess the results. The script would be similar to: from chimerax.core.commands import run run(session, "alphafold predict %s" % sequence_data) # wait until alphafold is done # and postprocess the file best_model.pdb but I do not know how to implement the part "wait until alphafold is done" if, after launching alphafold, I create a loop similar to: === counter = 0 current_size = _getSize(file_path) while current_size !=_getSize(file_path) or _getSize(file_path)==0 or not os.path.exists(file_path): current_size =_getSize(file_path) time.sleep(60) counter += 1 if counter > 240: # break after four hours if file is not created break ==== the loop is executed as soon as the alphafold command has been sent to google, the alphafold-colab window is not shown until the loop is finished and therefore, alphafold execution never starts. So the question is: how can I write a script that waits until the command "alphafold predict ..." finishes and then executes some code. Thanks Roberto

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Re: [chimerax-users] error with open :: 'foreach' has no suffix
by Eric Pettersen 15 Feb '22

15 Feb '22

Yes, that was quite helpful. The 'foreach' option only became available starting with the 1.3 release. You are running 1.2.5, so you need to upgrade. --Eric > On Feb 14, 2022, at 3:35 PM, Rangarajan, Amith <Amith.Rangarajan(a)ucsf.edu> wrote: > > This Message Is From an External Sender > This message came from outside your organization. > hi Eric, > > i have submitted a bug report > > > thanks > amith > From: Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> > Sent: Monday, February 14, 2022 3:15 PM > To: Rangarajan, Amith <Amith.Rangarajan(a)ucsf.edu <mailto:Amith.Rangarajan@ucsf.edu>> > Cc: ChimeraX Users Help <ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu>> > Subject: Re: [chimerax-users] error with open :: 'foreach' has no suffix > > This Message Is From an External Sender > This message came from outside your organization. > Hi Amith, > I don't care so much about the contents of your script per se — I'd like to see the contents of the log when the error occurs. Do this: run the command that generates the "'foreach' has no suffix" error and then use Help→Report A Bug and submit a bug report. That will include the contents of the log, which is what I need to see. Thanks! > > --Eric > >> On Feb 10, 2022, at 4:52 AM, Rangarajan, Amith <Amith.Rangarajan(a)ucsf.edu <mailto:Amith.Rangarajan@ucsf.edu>> wrote: >> >> This Message Is From an External Sender >> This message came from outside your organization. >> Dear Tom and Eric, >> >> I used notepad ++ to make sure that the cxc file was not a .txt ( i am on windows) and i am still getting the error ( foreach has no suffix) . i have attached my .cxc script . >> >> I am trying to read a set of .mae files and write a log file with RMSD and some distance measurements. >> >> I am new to chimera and would benefit a lot from your review of my script and possible fixes for this issue. >> >> thank a lot for your time. >> >> best regards, >> amith >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Tuesday, February 8, 2022 10:36 AM >> To: PETTERSEN, ERIC <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> >> Cc: Rangarajan, Amith <Amith.Rangarajan(a)ucsf.edu <mailto:Amith.Rangarajan@ucsf.edu>> >> Subject: Re: [chimerax-users] error with open :: 'foreach' has no suffix >> >> This Message Is From an External Sender >> This message came from outside your organization. >> Hi Eric, >> >> Not quite sure I understand your theory abut Amith's error. In current ChimeraX daily build using non-existent files with open command >> >> open something.cxc foreach somethingelse.py >> > No such file/path: something.cxc >> >> gives a very sensible error message and does not try to interpret "foreach" as a file name. >> >> Tom >> >>> On Feb 8, 2022, at 9:40 AM, Eric Pettersen via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hi Amith, >>> That error message indicates to me that the first file name (script.cxc) isn't being recognized as a ChimeraX command script file. So take a hard look at the command you typed and make sure that the suffix for that file is ".cxc" and not something mistyped like ".cxs" or whatnot. >>> >>> --Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>> >>>> On Feb 8, 2022, at 6:25 AM, Rangarajan, Amith via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> >>>> This Message Is From an External Sender >>>> This message came from outside your organization. >>>> Hi, >>>> >>>> I am trying to run a script and want to use foreach ( open script.cxc foreach *.pdb) to iterate through several pdb files in the working directory. >>>> >>>> I had no issues with running it earlier, but since last few tries, i am getting an error stating that ""'foreach' has no suffix"" >>>> >>>> I am not able to figure out how to debug this. >>>> >>>> I am using the latest build of chimerax. >>>> >>>> I will highly appreciate your suggestions on fixing this. >>>> >>>> best >>>> amith >>>> _______________________________________________ >>>> ChimeraX-users mailing list >>>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>>> Manage subscription: >>>> https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users> >> <RMSD-distance-final.cxc>

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Re: [chimerax-users] error with open :: 'foreach' has no suffix
by Rangarajan, Amith 14 Feb '22

14 Feb '22

Dear Tom and Eric, I used notepad ++ to make sure that the cxc file was not a .txt ( i am on windows) and i am still getting the error ( foreach has no suffix) . i have attached my .cxc script . I am trying to read a set of .mae files and write a log file with RMSD and some distance measurements. I am new to chimera and would benefit a lot from your review of my script and possible fixes for this issue. thank a lot for your time. best regards, amith ________________________________ From: Tom Goddard <goddard(a)sonic.net> Sent: Tuesday, February 8, 2022 10:36 AM To: PETTERSEN, ERIC <pett(a)cgl.ucsf.edu> Cc: Rangarajan, Amith <Amith.Rangarajan(a)ucsf.edu> Subject: Re: [chimerax-users] error with open :: 'foreach' has no suffix Hi Eric, Not quite sure I understand your theory abut Amith's error. In current ChimeraX daily build using non-existent files with open command open something.cxc foreach somethingelse.py > No such file/path: something.cxc ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Hi Eric, Not quite sure I understand your theory abut Amith's error. In current ChimeraX daily build using non-existent files with open command open something.cxc foreach somethingelse.py > No such file/path: something.cxc gives a very sensible error message and does not try to interpret "foreach" as a file name. Tom On Feb 8, 2022, at 9:40 AM, Eric Pettersen via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Amith, That error message indicates to me that the first file name (script.cxc) isn't being recognized as a ChimeraX command script file. So take a hard look at the command you typed and make sure that the suffix for that file is ".cxc" and not something mistyped like ".cxs" or whatnot. --Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 8, 2022, at 6:25 AM, Rangarajan, Amith via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: This Message Is From an External Sender This message came from outside your organization. Hi, I am trying to run a script and want to use foreach ( open script.cxc foreach *.pdb) to iterate through several pdb files in the working directory. I had no issues with running it earlier, but since last few tries, i am getting an error stating that ""'foreach' has no suffix"" I am not able to figure out how to debug this. I am using the latest build of chimerax. I will highly appreciate your suggestions on fixing this. best amith _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

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Models panel selecting
by William Hofsøy 14 Feb '22

14 Feb '22

Hi, The checkboxes for selecting models in the "Models" panel can't select multiple models without first selecting their parent model and then unchecking all the other models. So I would like to request that it would be possible to select multiple models somehow, either shift clicking or maybe just by default as is what I would expect from them being checkboxes. Best Regards, William

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Error reported by AlphaFold
by Juntao Yu 14 Feb '22

14 Feb '22

Dear ChimeraX community, I am a graduate student from Harvard Medical School who recently became interested in using AlphaFold-Multimer to predict protein complex structures of my interest. I have been tried a few times of predicting one protein complex and I was able to finish all MSA. However, when AlphaFold starts predicting the structure, all five models were reported as “error”. It is surprising to me because it is known that these two proteins should form a complex. I noticed in the script on the line is: “print ('\nAlphaFold generated an error computing %s, error logged to %s\n'% (model_name, error_log_path))”. The results printed exactly what this line says. I am wondering whether it means the Multimer is not able to predict this complex structure? Is there any tutorial that I can find to change parameters in order to try to improve and get a structure? Thanks, Juntao ------------------------------------------ Juntao Yu | Ph.D. candidate Moazed Lab Department of Cell Biology Harvard Medical School 240 Longwood Avenue Boston, MA 02115

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Issues with download
by Clara Kjerfve 14 Feb '22

14 Feb '22

Hello, I have downloaded the updated daily version of your software but am unable to open the app. I have updated to the newest software and still not able to open it. Can you please send me some steps on how to proceed. Thank you. Clara Kjerfve

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color submodels using a palette
by vincent Chaptal 14 Feb '22

14 Feb '22

Dear all, I have a pdb with 20 submodels inside (NMR type) that opens well in chimeraX. I would like to color each submodels individually, using a palette accross these models. For example from model #1.1 in red to model #1.20 in blue. I couldn't find the command online, does it exist in ChimeraX? Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Re: [chimerax-users] python script for measuring distance
by Rangarajan, Amith 13 Feb '22

13 Feb '22

Hello everyone, Please see my script below: import os import sys from chimerax.core.commands import run as rc target_folder = '/wynton/home/jacobson/avranga1008/Documents/0-combo' os.chdir(target_folder) home =os.getcwd() all = os.listdir() xp_distance_file = os.path.join(home,'xp-distance.log') print_to_screen = sys.stdout mae_files =[] for f in all: if f.endswith('.mae'): mae_files.append(f) print(f'working on {f}') sys.stdout = open(xp_distance_file,'a') rc(session,"open " + f) rc(session,"measure center #1.1 & ligand mark true") rc(session,"measure center #1.1 :310,335,728,759 mark true") rc(session,"distance #2 #3") rc(session,"close") sys.stdout = print_to_screen print(f'completed writing xp-distance values to {xp_distance_file} ; now moving to next loop') for f in mae_files: line = f + '\n' open('file_list.txt','a').write(line) print("loop is complete") exit() I am curently using stdout to write the distance values to a file .I am currently running it on command line [cid:68afa919-1a35-470f-808c-242e97c85957] it seems like a round about way to do it. The output file has lot of special characters and it takes a bit of effort using regex to extract the values. I think there might be some logger in chimerax which can do this or some other better way to write results to a file , but i am not able to find it. ############# please let me know your suggestions on improving this code. thanks, amith

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Re: [chimerax-users] Chimera system requirements
by Elaine Meng 10 Feb '22

10 Feb '22

> On Feb 10, 2022, at 10:03 AM, Armin Delnia <armindelnia(a)gmail.com> wrote: > > Dear Sir/Madam, > I would like to ask what are the system requirements in order to run Chimera and ChimeraX in terms of the RAM and CPU specifications? Thank you. > Regards, > Armin Delnia Hello Armin, This e-mail address is for commercial licensing requests. For questions about using the program(s) we recommend chimerax-users(a)cgl.ucsf.edu and/or chimera-users(a)cgl.ucsf.edu. <https://rbvi.ucsf.edu/chimerax/docs/contact.html> <https://www.rbvi.ucsf.edu/chimera/docs/feedback.html> I don't have a specific answer for you, but I CC'd chimerax-users(a)cgl.ucsf.edu on this message so you don't need to do anything else this time. I only have the following general information: the download pages say which operating systems are supported for running the programs. The ChimeraX download page also recommends using a computer <4 years old. <https://www.rbvi.ucsf.edu/chimerax/download.html> <https://www.rbvi.ucsf.edu/chimera/download.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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How to define axes in chimeraX
by Zhao, Bingchun (NIH/VRC) [F] 10 Feb '22

10 Feb '22

Hi, I’ve been using Chimera to define the axes of my model, then to calculate the angle of approach, by using Tools • Structure analysis • Axes/Planes/Centroids • Define axes But I wasn’t able to find out the equivalent function in chimeraX. Would you please direct me to that function in ChimeraX? Thank you so much! Best regards, Bingchun Bingchun Zhao, PhD Postdoctoral, VF Biodefense Research Section VRC/NIAID/NIH Bldg 40, Room 2607B 40 Convent Drive Bethesda, MD 20892 Tel: 301-761-7649 Email: bingchun.zhao(a)nih.gov<mailto:bingchun.zhao@nih.gov>

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Show atom style as spheres and stick simultaneously
by Mary Liu 10 Feb '22

10 Feb '22

Dear Chimera X users, Is it possible to show atom style as spheres and stick simultaneously with spheres displayed as dots or mesh so the stick is still visible within sphere dots? Thank you Mary

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Loading AlphaFold output
by Daniel Trejo Banos 10 Feb '22

10 Feb '22

Hello everyone, I have the results from some AlphaFold runs, is there a way to open them with ChimeraX, so I can see the plDDT, without needing to run Alphafold from within ChimeraX? Thank you and best regards

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bonding Question
by Noriega, Heather 09 Feb '22

09 Feb '22

Hello, I hope you are well. I have a quick question about the bond command. I attached the pdb file I have been using to try and learn this command. I am having a hard time figuring out how I should write it on the command line. If I want to create a bond between residue Lys76 from the antibody and the Oxygen #2 from my polymer, how would I write it on the command line? bond :lys76:O2 I have read the section in the manual but I think I am misunderstanding something, it keeps giving me a mangled atom specifier. Also, I figured out the problem from my last question/email about the volume in my viral capsid. :) Thank you for your help on that one Elaine. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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Pseudo bonds of missing structure in cartoon style
by Wout Oosterheert 09 Feb '22

09 Feb '22

Dear ChimeraX team, I’m making figures of a protein structure that has 4 residues missing in a flexible region. When I show the atoms as “style stick”, I can see a dashed pseudo bond between the two residues that connect the missing segment. However, when I “show cartoons” of the same structure, the dashed line disappears and the pseudo bond is no longer visible. Would you have any suggestions on what to change to make the missing structure appear as a dashed line when the model is shown in cartoon style? Of interest, in a similar structure where 3 instead of 4 residues are missing, the dashed line is in fact shown when the model is shown in cartoon style. In addition, in regular Chimera the dashed line that represents the 4 missing residues remains visible in cartoon style. Thank you for your time. Best wishes, Wout Wout Oosterheert, PhD Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany Phone +49-(0)231-133-2357 Email: wout.oosterheert(a)mpi-dortmund.mpg.de<mailto:wout.oosterheert@mpi-dortmund.mpg.de>

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Keep color on vseries
by Eric Pettersen 08 Feb '22

08 Feb '22

> > From: "Hunkeler, Moritz" <Moritz_Hunkeler(a)DFCI.HARVARD.EDU <mailto:Moritz_Hunkeler@DFCI.HARVARD.EDU>> > Subject: Keep color on vseries > Date: February 8, 2022 at 8:20:31 AM PST > To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> > > > Hi, > > I am sure I am missing a simple step here, but I would like to visualize a vseries where each frame is colored according to an underlying model. So, I color all frames with ‘color zone #id near #id distance 15’ and then start the vseries with ‘loop true’ and ‘maxFrameRate 2’. However, as soon as it loops around once, the coloring of all maps is set back to the starting default color. Same thing happens if I just start the vseries twice without ‘loop true’: during the first round, all maps are colored correctly, during the second round all map coloring is reset. This seems to happen only when started from the command line, and not when started from the vseries slider. Is it possible to keep the map coloring when starting the vseries from the command line? I am using the version released 20220204. > > Best, > Moritz

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Re: [chimerax-users] error with open :: 'foreach' has no suffix
by Rangarajan, Amith 08 Feb '22

08 Feb '22

Hi, I am trying to run a script and want to use foreach ( open script.cxc foreach *.pdb) to iterate through several pdb files in the working directory. I had no issues with running it earlier, but since last few tries, i am getting an error stating that ""'foreach' has no suffix"" I am not able to figure out how to debug this. I am using the latest build of chimerax. I will highly appreciate your suggestions on fixing this. best amith

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Extract densities option not available on Segment Map
by Andre LB Ambrosio 08 Feb '22

08 Feb '22

Dear all, probably a silly question: I want to generate a mask o ChimeraX to use later on a local refinement job elsewhere. I managed to segment the cryoEM map and group the regions of interest. However, the "Extract densities" option is unavailable on the "Regions" menu. Likewise, these are unavailable on "Other tools" shortcuts options: Extract, iSeg, ProMod, and ModelZ. Please, what am I missing? I appreciate any help you can provide. -- Andre LB Ambrosio Associate Professor, IFSC/USP - Brazil www.ifsc.usp.br/alba

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extraction of certain cryo-em density
by Dmitry A. Semchonok 08 Feb '22

08 Feb '22

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Next/previous buttons?
by Oliver Clarke 07 Feb '22

07 Feb '22

Hi, The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? Cheers Oli PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc?

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keeping multi-chain models locked between chains
by Martti Tolvanen 07 Feb '22

07 Feb '22

Dear ChimeraX gurus and demi-gods, I have created a hypothetical multimer model for a protein which has a dimeric structure in PDB (with a large protein-protein interface, considered real), but misses the C-terminal part of the full protein sequence. AlphaFold predicts there to be an amphipathic helix in the missing part, as we also did in our theoretical work. The hypothesis is that the protein could form larger multimers by binding either via the face-face interactions, as in the PDB dimer of catalytic domains, or via helix-helix interactions (tail-tail) as in coiled coils, to create multimers of type AB-BA-AB-BA-AB-BA etc., A being the helical domain and B the catalytic domain. I have created antiparallel coiled-coil-like helix dimers from the helix predicted by AlphaFold with the help of zdock (big thanks for adding the zdock file open functionality in the daily build!) and built a hexamer model using 3fe4 and my best-looking zdock helix pair as templates for orienting the six copies of the monomeric alphafold model. The helix is randomly placed outside of the confident catalytic domain structure in the AlphaFold model, and there is a linker of poor confidence between the domains. With the original orientation of the helix my first-effort hexamer has the catalytic domains partly overlapping, and I'd need to rotate some bonds manually to orient the subunits into realistic positions. I wouldn't care even if I create some serious Ramachandran plot outliers there, when the goal is just to get a visualization for the multimer hypothesis. The problem is that when I rotate any bond in the linker, I either swing one helix out of a coiled-coil pair or one catalytic domain out of the face-to-face dimer interface (depending if I use move small of move large, respectively, in the torsion command). How could I get all six chains into a single chain? I assume that then I would be moving the whole rest of the multimer as a rigid body if I rotate any main-chain bond in the linker regions. ChimeraX session file attached. Cheers, -Martti Tolvanen U of Turku, Finland

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Re: [chimerax-users] chimeraX on wynton ( UCSF-specific)
by Rangarajan, Amith 04 Feb '22

04 Feb '22

Hi, This question is relevant for UCSF only. I have a set of docked poses that i want to analyze using chimera x script ( check ligand RMSDs, distances etc...) . My laptop is not that great, so i can use Wynton, if possible, to do this . is chimerax available on Wynton nodes? if so, please give me a short intro to get started on using chimerax on Wynton. thanks, amith I

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Automate calculation and saving of residues' structural attributes
by André 04 Feb '22

04 Feb '22

Hello! I'm working on an automated pipeline (in Python) for the structural analysis of proteins. In particular, I'm using Chimera to calculate and save to .txt files some structural properties of residues (namely: areaSAS, areaSES, relSESA, bfactor, kdhydro, phi, psi). These files are the inputs of the pipeline. However, currently the files are exported manually, and, for the purpose of building a fully automated pipeline, it would be great to also automate this step of calculating the attributes and exporting their respective files. I searched a lot, and tried some ways to achieve such an automation (using Chimera), but nothing worked. And I also considered using ChimeraX. In particular, I went through ChimeraX Programming Manual ( https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html#) but, if I understood correctly, I'd only be able to import chimerax and use its functions in the Python interpreter within ChimeraX (Tools >> General >> Shell). At first, I'd like to import chimerax as a module in a Python interpreter outside of ChimeraX, so that manually opening ChimeraX wouldn't be necessary in order to save the files with the residues' attributes. But, from some other threads in the mailing list, I found that it wouldn't be possible (right?) But I also found out that I could write a .py script which calculates and exports the files with the residues' properties, and then run it with ChimeraX application from the command-line, something like: *chimerax --nogui myscript.py* If that works, I think that my automation problem would be solved! The only problem is that I really couldn't figure out the Python code to calculate and export the aforementioned residues' properties (I took a look in ChimeraX Recipes (https://rbvi.github.io/chimerax-recipes/) but I couldn't find what I need, nor more detailed documentation). Given that, I'd like to know if anyone has done something like this, and/or have any guidance on how I could proceed. I really appreciate any help you can provide! (And thanks to Tom Goddard for suggesting moving the discussion here to the ChimeraX mailing list). Thank you so much, André.

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Is there an output directory command for spin movies or morphs?
by Ralph Loring 03 Feb '22

03 Feb '22

Hi, I've given my students an assignment due on Monday which includes making a spin movie. About a third of the class tells me that they can see the molecule spinning while the movie is compiling, but that they can't find where the mp4 file goes. I have no trouble using my laptop, but if I use my office desktop computer, I have the same problem (see picture). The first two error messages were endogenously generated by ChimeraX, the last 3 were me trying to force the output directory. When I spoke to our IT people, they informed me that university computers are not allowed to save files to the public desktop, but prefer that it go to the user desktop in Onedrive. My question is whether there's a command that I can give before running a spin movie that specifies in what directory the output file should be put? Thanks, Ralph Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu

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Change default palette for sequential coloring?
by Oliver Clarke 03 Feb '22

03 Feb '22

Hi, I really like the option to use custom palettes from colorbrewer etc in ChimeraX for sequential coloring. Would it be possible to allow users to change the palette used as the default for sequential coloring? E.g. I really like "RdYlBu-5 (3-11)", but I can never remember the name or syntax, and for quick jobs I would love to be able to to set the default coloring scheme so it is just set up the way I like it. Cheers Oli

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Coloring Chains Sensitive to Case After Combine
by Anderson, Jacob 03 Feb '22

03 Feb '22

Dear ChimeraX, Really loving the implementation of the combine command in 1.3! After using the combine command to create a model with >30 chains, the resultant model has some chains with the same chain ID but with a lowercase (i.e. #6/D and #6/d are in the model). When I color #6/D (i.e. color #6/D green), this also is coloring chain #6/d. Is this the expected behavior? When I read help:user/commands/atomspec.html it seems that the chain identifier should be case sensitive if both upper and lowercase chain IDs are present. Curious if there is a way to force the case sensitivity.

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"Backbone N-H atoms” as Ball & Stick representation
by Gupta, Arun 02 Feb '22

02 Feb '22

Hello Elaine and team, I am working with Chemical shifts based CS-Rosetta generated NMR structural model of the protein (amino acid sequence 1-84). And, I would like to show the “backbone N-H atoms” in the NMR structural model in a ball & stick representation. The series of command which I have used are as follows Open pdb cartoon suppress false sel #1:1-84 @n,h And finally from ChimeraX GUI interface, I am choosing following set of options Action/Atom style/ Ball & Stick. But nothing happens. It seems I am missing something. Please suggest the way around with this problem. Thanks! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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Default Save Location
by William Wang 02 Feb '22

02 Feb '22

Hi ChimeraX Team. Is there anyway to set the default location for the save command as somewhere other than desktop? Thank you William Wang Undergraduate Student Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Building ChimeraX Bundle
by Zeng, Katie 01 Feb '22

01 Feb '22

Dear ChimeraX Users, I'm currently working on a bundle for building lipid membranes and I have a few questions: 1. A part of my bundle is a lipid selector that works with AMBER-compatible pdb files. I followed the tutorial and have successfully built a selector that selects all lipids of the type I specify (say, I put in the command line 'sel POPC' then all the POPCs in the membrane get highlighted). Because of the way AMBER lipid forcefields work, individual lipids are separated into three residues, one head and two tails. I'm trying to add a function to my bundle such that individual lipids can be selected - e.g. when I select a headgroup and go [up]+[up], then the entire lipid can be selected. How can I group three residues together in a bundle? 2. Is it possible to register multiple selectors through a single function? There are many lipids that I want to include in the selector, but for now I have to copy the same function over and over if I want to do that. It will be great if I could have a list containing all the names of the lipids and have a function that registers all of them. 3. Are there any built bundles that are open source? I tried to access the source code of bundles after installing them but I couldn't find the directory of which they are stored. It will be really helpful if I could refer to them. Thank you so much for your help! Best Regards, Katie

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hbonds and the number of detected interactions
by Enrico Martinez 31 Jan '22

31 Jan '22

Dear ChimeraX users! I have a question regarding calculations of the hydrogen bonds and its visualisation using hbonds. Here is my command: hbonds #1 & ligand reveal true log true radius 0.06 dashes 6 color turquoise distSlop 0.4 angleSlop 20 intraRes false So I ignore intraRes (since the ligand is also present in the #1) and calculate hydrogen bonds using default parameters. 1) How can I modify geometric criteria for the calculations (is this distSlop / angleSlop) to increase the distance for the consideration of potential h-bonds ? In particular as you may see on the attached image the bond between the side-chain of the Glu166 and NH of the ligand is absent (I've just checked the same structure using py*ol and it could detect this contact). 2) In the case of another ligand, I could visualize two h-bonds provided by two hydrogens of the side chain of the Gln189 (same residue) with two different oxygens of the ligand. Is this correct? Many thanks for the tips! Yours sincerely Enrico

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ChimeraX 1.4 Download?
by Nayla Abney 27 Jan '22

27 Jan '22

Good evening, Hope you are doing well! I am trying to use your ChimeraX 1.4 download after watching this AlphaFold Protein Complex via ChimeraX Youtube video (https://www.youtube.com/watch?v=6lXeCPuTePs) However, I am having issues finding the download for the 1.4 version because your website only shows the 1.3 download (https://www.rbvi.ucsf.edu/chimerax/download.html) When I try using this version, I am having issues with inputting the sequence in the correct format because I keep getting a sequence argument error. I have tried looking up documentation for this version and this error, however, I am only seeing 1.4 documentation. Could you guide me in the right direction of where I should go ideally for the 1.4 download? I guess my Googling skills could use some help :) Thank you! ------------------------------------------------------ Nayla

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Help viewer is blank after upgrading to Fedora 35
by Nicholas R Silvaggi 26 Jan '22

26 Jan '22

Hello, I am just getting started with ChimeraX. I installed the latest production release (Centos 8 version, ucsf-chimerax-1.3-1.el8.x86_64) on my Fedora 33 workstation. It worked great. I installed Isolde and Clipper through the help viewer winder and everything was great. Yesterday I upgraded the operating system to Fedora 35, and now the help viewer no longer works. It is just blank. I can't get it to show other web sites, files from my hard drive - nothing. I installed ChimeraX on 3 other workstations, and all have the same problem. This is very curious and there is no error output that I can find to help point me to the problem. Has anyone else experienced this? Thanks for your help, Nick Silvaggi P.S. I also tried uninstalling the production release and installing the Centos 8 version of the latest nightly build - same problem persists. Nicholas R Silvaggi, Ph.D. University of Wisconsin, Milwaukee Department of Chemistry and Biochemistry 3210 North Cramer St Milwaukee, WI 53211 Office: Chemistry 372D Phone: 414-229-2647 silvaggi(a)uwm.edu

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Modeller python script
by Mary Liu 26 Jan '22

26 Jan '22

Dear Chimera X team, I'm using Modeller in ChimeraX to build a homology model. Is there a way to look at the python script to know how it works? Thanks Mary

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3Dconnexion
by Wang, Difei (NIH/NCI) [C] 26 Jan '22

26 Jan '22

Hello ChimeraX team, Thanks for developing the ChimeraX! It is easier to use than Chimera. However, I noticed that my 3Dconnexion could not work anymore when I use ChimeraX. Will it be possible to include such a function in the future version of ChimeraX? Thanks, Difei ======================== Difei Wang, Ph.D. Bioinformatician (Contractor) BB/DCEG/NCI/NIH 9609 Shady Grove Rd. Rockville MD 20850 USA Tel: 1-240-276-5092 ========================

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Surface coloring
by Enrico Martinez 26 Jan '22

26 Jan '22

Dear ChimeraX users! I am working on the protein-ligand binding visualizations using surface representation for the protein. In this case (please see enclosed example) I used mlp palette moccasin:sienna:sandybrown range -55,55 to make this expression of the protein in the Mountain style :-) Two questions: 1) how can I introduce more "dark" gradients into the cavities (similar to the vulcan) ? 2) is it possible to switch the coloring pattern from such a "realistic" view to the animated "cartoon" style ? 3) Any additional advice for the surface visualisations ? Many thanks in advance! Enrico

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artistic cartoon visualisations
by Enrico Martinez 26 Jan '22

26 Jan '22

Dear ChimeraX users! I am working on the improvement of the cartoon visualizations. Here are some options that I have found very cool: preset 'overall look' publication cartoon style coil thickness 0.22 set silhouettes t; set silhouetteColor firebrick; set silhouetteDepthJump 0.02 could you please suggest me something, which may further develop these ideas? In particularly I would like to improve representations of the beta-sheets making the arrow-ends more elongated and cylindrical Many thanks in advance Enrico

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Debian 10 Installation
by Martin Urban 25 Jan '22

25 Jan '22

Dear ChimeraX users, I have a problem with the installation of ChimeraX under Debian 10 buster. I downloaded the ucsf-chimerax_1.3ubuntu18.04_amd64.deb from the official website. I installed it one time with: /sudo dpkg -i //ucsf-chimerax_1.3ubuntu18.04_amd64.deb /and also with /sudo apt-get install .///ucsf-chimerax_1.3ubuntu18.04_amd64.deb./ Both times I get the same error message: qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in " " even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. The full error message is as attachment in this mail. I searched the web for an answer and came up with three entries of this mailing list. I followed the described way in these mails, but nothing worked for me (1st mail: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002797.html; 2nd mail: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002770.html; 3rd mail: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-June/002339.html) Do you have an answer or a solution to my problem? Greetings from Germany -- Martin

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Ribbon Thicken
by Cameron Larson 25 Jan '22

25 Jan '22

Hello, Is there a way to thicken ribbons so I can 3d print a structure? What do you recommend for 3d printing a structure? -Cameron Larson

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Re: [chimerax-users] rename a ligand from UNK 999
by Rangarajan, Amith 25 Jan '22

25 Jan '22

Dear ChimeraX users, When i add a pdb file to chimera , the resulting model displays the ligand as UNK 999 and when i am having multiple models , it will help to be able to edit the UNK to name the ligand. is there a way to do it ? thanks , amith

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Displaying secondary structure elements
by Enrico Martinez 25 Jan '22

25 Jan '22

Dear ChimeraX users! Could you suggest to me the command which will 1) hide all loops from the selected object? 2) hide all loop regions which contain more than 10 residues (=hide long loops)? Thank you in advance! Enrico

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Surface representation of protein-ligand interactions
by Enrico Martinez 25 Jan '22

25 Jan '22

Dear ChimeraX users! I am working on the surface representation of the protein-ligand contacts. Here is my script: # load pdb of the complex and keep inly the 1st model open pdb.pdb close #1.2-end #calculate electrostatic surface coulombic protein key true #change view of the ligand size ligand atomRadius +.8 color #1.1 & ligand & C gold style ligand sphere #protein-ligand contacts hbonds #1.1 & ligand reveal true log true contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange ~label ligand hide #1 & protein bonds hide #1 & protein pseudobonds Here are my questions: 1) is it possible to set transparency on the part of the displayed surface that overlaps (hide) with the part of the displayed ligand? i've tried: transparency 20 surface, but it change the transparency for whole surface 2) how I may improve further sphere representation of the ligand? it looks very nice but probably there are further modifications ? 3) is it possible to customize the following commands to display amino-acids that within specified distance within the ligand (I would like to display only very closer amino-acids): contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange Many thanks in advance! Cheers Enrico

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Color atoms by RMSD
by Nebojsa Bogdanovic 21 Jan '22

21 Jan '22

Hello, I am looking to color the atoms (cartoon representation) by RMSD values obtained from the matching of the two structures. Is there such a function? I would like to show which part of the target domain is moving the most in comparison to the previously x-ray solved structure of a know ligand state without showing the actual structures overlaid. Thank You very much. Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Assessment of labeling data using ChimeraX
by Alessio Di Ianni 20 Jan '22

20 Jan '22

Respectable ChimeraX developers, how can I visualize labeling data obtained by Mass Spec Studio into a pdb structure using ChimeraX? A help will be definitely appreciated. Best regards Alessio Di Ianni PhD Student Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entance C D-06120 Halle/Saale Tel: +49 (0)345 55 25224

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selecting and translating / rotating 1 of the models/maps
by Dmitry Semchonok 20 Jan '22

20 Jan '22

Dear colleagues, Quick question. In chimeraX, with multiple models, how can I select and rotate/translate only one/ or two of them? In chimera it was possible to make the selection in the model panel. Kind regards, Dmitry

2 1

view and the center of mass of the selection
by Enrico Martinez 20 Jan '22

20 Jan '22

Dear ChimeraX users! I am using view command to center the camera on the ligand an then, to rotate th whole system to the desired position: view #1.1 & ligand orient clip false; turn z 90; turn y 45; turn x -90; turn x 77 may I rather center the camera on the center of mass of the ligand calculated using measure center ligand If so, how may I combine the both commands together? Thank you in advance! Enrico

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Feature requests
by Ishwar Radhakrishnan 19 Jan '22

19 Jan '22

Hello - I would like to request two features in ChimeraX that we use a lot in Chimera: 1. Render by Attribute 2. Ability to read .poc files created by CASTp Thanks, Ishwar

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service unavailable for toolshed
by Bharti Singal 18 Jan '22

18 Jan '22

Hi , I am trying to install isolde and clipper tools on chimerax 1.3 but the toolshed is giving error for last 24 hours "service unavailable". Is it possible to get the download link of these two tools as I need them for some urgent work? Best regards, Bharti Singal Bharti Singal, Ph.D. Postdoctoral Scholar (Al-Bassam's Lab) Department of Molecular and Cellular Biology| College of Biological Sciences| University of California, Davis| 605 Hutchison Dr, Davis, CA 95616, USA

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labeling of protein-ligand interactions
by Enrico Martinez 18 Jan '22

18 Jan '22

Dear ChimeraX users! I am working on the visualization of the protein-ligand interactions. The two below commands are used to visualize and label amino acids involved in the interactions with the ligand contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display How could I increase the font size and change the colour of the displayed amino acid labels (like Tyr-188)? Is it possible to hide the name of the ligand which always appears after the label command? Many thanks in advance! Enrico

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Alphafold multimer
by Rafael Ponce 17 Jan '22

17 Jan '22

Dear Sir or Madam, I want to predict the structure of a complex in ChimeraX using alphafold, but it seems that this feature is going to be in version 1.4 but version 1.3 is the one that is currently available, so I would like to know if you have an estimation of when the version 1.4 will be available to download. Thank you in advance for the information. Best regards, Rafael Ponce

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zoom on the selection after orientation of the selected object
by Enrico Martinez 17 Jan '22

17 Jan '22

Dear Chimera users! I am using ChimeraX for the visualization of protein-ligand interactions comparing two different pdb structures A - ensemble for doclong; B- X-ray pose: open A.pdb open B.pdb' match #2 to #1.1 # close all docking poses with the exemption of the first pose: close #1.2-end view wait # hide the protein from X-ray pose keeping only ligand for visualisation: hide #2 & protein cartoon hide #2 & protein surface hide #2 & protein #orient view on the model 1.1 and zoom closer view #1.1 orient; turn z 90 zoom 1.5 wait The problem is that when I use zoom 1.5 after view #1.1 it hides completely the representation for the molecule on the current GUI. Otherwise, it works fine if I center view on the both A and B: view orient; turn z 90 zoom 1.5 How could I zoom the screen properly after orientation of the view on the first molecule? Many thanks in advance! Enrico

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Cleaning a pdb file
by Martin Urban 16 Jan '22

16 Jan '22

Hey there, I have a specific pdf file (3BMP.pdb) and I would like to "clean" it from the chemical compounds which are in the file. I would like to know if there is anyway in ChimeraX to "clean" the file programmatically? Greetings from Germany - Martin

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Re: [chimerax-users] [Chimera-users] ChimeraX in no-gui mode: visualisation of protein-ligand interactions
by Elaine Meng 16 Jan '22

16 Jan '22

See the "color" command for coloring the ligand, and "set" or "graphics" for coloring the background, and "label" (or "2dlabels" but that usually requires you to position them interactively) for labeling. All of these are included in the "making images" page I mentioned near the end of my previous message. Best, Elaine > On Jan 14, 2022, at 3:03 PM, Enrico Martinez <jmsstarlight(a)gmail.com> wrote: > > Thank you very much, Elaine! > I really like ChimeraX and it looks so great for me with all of those > presents :-) I will look for the details regarding the options. Just a > few addtional questions regarding customizing representation of > protein-ligand interactions using ghost preset: > In particular: I would like to color ligand (in orange??) > To add labels (like Try-193) on the displayed side-chains around the ligands > To change background from black to indigo! > :-) > Many thanks in advance! > Cheers > Enrico > > пт, 14 янв. 2022 г. в 23:48, Elaine Meng <meng(a)cgl.ucsf.edu>: >> >> Hello, >> It isn't my area of expertise, but I don't think you can save images in nogui mode except with Linux OSMesa. >> >> As for your other questions, which commands do certain things... >>> may you suggest some commands that I may introduce into my batch file to >>> 1) delete all models from the multi-model pdb file with the exemption >>> of the first model. >>> 2) switch from cartoon to surface representation of the protein >>> 3) visualize protein-ligand non-covalent interactions in the current model >> >> >> (1) close submodels except for first one. Maybe something like command: >> >> close #1.2-end >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/close.html> >> >> (2) switch from ribbon to molecular surface of protein. Well, you probably want to do some coloring and other stuff besides just hiding ribbon and showing surface, which could be something like commands: >> >> ~ribbon >> surface protein >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> >> >> Or you could try a surface-showing preset, e.g. >> >> preset ghost >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/preset.html> >> >> (3) depends what you mean by showing interactions (lines? selection? coloring?). You should take a look at commands "contacts" and/or "hbonds" and choose the options that give what you want. >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html> >> >> You will need to spend some time trying the commands since there are an infinite number of possibilities for combinations of coloring and display styles and lighting and graphics effects. See also commands "lighting" and "graphics" and "set" >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html> >> >> ... and the "making images" page with several relevant commands >> <https://rbvi.ucsf.edu/chimerax/docs/user/images.html> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >>> On Jan 14, 2022, at 2:17 PM, Enrico Martinez via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >>> >>> Dear Chimera's users! >>> First I wish Happy New Year to everyone! >>> I am just switching from Chimera to ChimeraX that I am going to use in >>> no-gui (batch) mode to prepare screen shots of protein-ligand >>> interactions based on the protein-ligand docking poses. Basically I am >>> loading a pdb file of the complex (consisted of protein and ligand in >>> multi-model format) from the terminal of my macOSX. I have a template >>> for a batch file created in the bash script on the fly, that I used 2 >>> years ago with an early version of ChimeraX. >>> >>> # a batch file for chimeraX >>> printf "open ${pdb} >>> view; zoom 1.0; turn x 90; turn z -80; >>> wait >>> # options for appearance >>> preset 'overall look' publication >>> # set bg powder blue >>> set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02 >>> >>> # make info of the screen >>> 2dlab create title text \"${pdb_name}\" color red font gothic xpos .04 >>> ypos .92 size 35 >>> >>> # options for light >>> light depthcuestart .4 depthcueend .8; lighting full intensity 1.4 >>> shadows true qualityOfShadows finer >>> >>> save image ${structure}/${pdb_name}.png format png width 800 height >>> 600 supersample 4 transparentBackground false >>> wait >>> exit" > chimeraX.${pdb_name}.cxc" >>> >>> then I use it directly in terminal as >>> chimerax-daily chimeraX.${pdb_name}.cxc" >>> >>> may you suggest some commands that I may introduce into my batch file to >>> 1) delete all models from the multi-model pdb file with the exemption >>> of the first model. >>> 2) switch from cartoon to surface representation of the protein >>> 3) visualize protein-ligand non-covalent interactions in the current model >>> >>> Yours with thanks >>> Enrico >> >

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Color Model by Another Model
by Anderson, Jacob 15 Jan '22

15 Jan '22

I have a use case where I would like to color chains of model X by the chains of model Y (they are duplicates). What might be the best way to do this? For example, I thought there may be a way to run something like: "info colors #1 byChain" to get the colors of all chains printed to the log like "#1/A blue, #1/B red . . .". Then one could easily change #1 to #2 with sed in a text editor. Does a tool like that exist in ChimeraX? Or has might anyone have tips for coloring a model's chain by another models chains? jacob

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Saving images in nogui mode
by Tom Goddard 14 Jan '22

14 Jan '22

Hi Erico, Greg is right that only Ubuntu and CentOS Linux ChimeraX versions include rendering images in no gui mode. But I made rendering in no gui mode work on macOS about a year ago, but it is not in the distribution because it is such a rarely used feature it did not seem worth increasing the distribution by 16 Mbytes. But I could provide this to individuals who need it. Tom > On Jan 14, 2022, at 3:05 PM, Greg Couch via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > That is correct. You would need to start ChimeraX with the --offscreen flag to be able to save images in nogui mode (offscreen implies nogui). And that only works with the Ubuntu and CentOS versions of ChimeraX. > > -- Greg > > On 1/14/2022 2:48 PM, Elaine Meng via Chimera-users wrote: >> Hello, >> It isn't my area of expertise, but I don't think you can save images in nogui mode except with Linux OSMesa. >> >> As for your other questions, which commands do certain things... >>> may you suggest some commands that I may introduce into my batch file to >>> 1) delete all models from the multi-model pdb file with the exemption >>> of the first model. >>> 2) switch from cartoon to surface representation of the protein >>> 3) visualize protein-ligand non-covalent interactions in the current model >> >> (1) close submodels except for first one. Maybe something like command: >> >> close #1.2-end >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/close.html> >> >> (2) switch from ribbon to molecular surface of protein. Well, you probably want to do some coloring and other stuff besides just hiding ribbon and showing surface, which could be something like commands: >> >> ~ribbon >> surface protein >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> >> >> Or you could try a surface-showing preset, e.g. >> >> preset ghost >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/preset.html> >> >> (3) depends what you mean by showing interactions (lines? selection? coloring?). You should take a look at commands "contacts" and/or "hbonds" and choose the options that give what you want. >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html> >> >> You will need to spend some time trying the commands since there are an infinite number of possibilities for combinations of coloring and display styles and lighting and graphics effects. See also commands "lighting" and "graphics" and "set" >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html> >> >> ... and the "making images" page with several relevant commands >> <https://rbvi.ucsf.edu/chimerax/docs/user/images.html> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >>> On Jan 14, 2022, at 2:17 PM, Enrico Martinez via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >>> >>> Dear Chimera's users! >>> First I wish Happy New Year to everyone! >>> I am just switching from Chimera to ChimeraX that I am going to use in >>> no-gui (batch) mode to prepare screen shots of protein-ligand >>> interactions based on the protein-ligand docking poses. Basically I am >>> loading a pdb file of the complex (consisted of protein and ligand in >>> multi-model format) from the terminal of my macOSX. I have a template >>> for a batch file created in the bash script on the fly, that I used 2 >>> years ago with an early version of ChimeraX. >>> >>> # a batch file for chimeraX >>> printf "open ${pdb} >>> view; zoom 1.0; turn x 90; turn z -80; >>> wait >>> # options for appearance >>> preset 'overall look' publication >>> # set bg powder blue >>> set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02 >>> >>> # make info of the screen >>> 2dlab create title text \"${pdb_name}\" color red font gothic xpos .04 >>> ypos .92 size 35 >>> >>> # options for light >>> light depthcuestart .4 depthcueend .8; lighting full intensity 1.4 >>> shadows true qualityOfShadows finer >>> >>> save image ${structure}/${pdb_name}.png format png width 800 height >>> 600 supersample 4 transparentBackground false >>> wait >>> exit" > chimeraX.${pdb_name}.cxc" >>> >>> then I use it directly in terminal as >>> chimerax-daily chimeraX.${pdb_name}.cxc" >>> >>> may you suggest some commands that I may introduce into my batch file to >>> 1) delete all models from the multi-model pdb file with the exemption >>> of the first model. >>> 2) switch from cartoon to surface representation of the protein >>> 3) visualize protein-ligand non-covalent interactions in the current model >>> >>> Yours with thanks >>> Enrico >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users >

1 0

Re: [chimerax-users] [Chimera-users] Autodock Vina plugin
by Ralph Loring 12 Jan '22

12 Jan '22

Hi, I've been trying out ChimeraX v. 1.3 vs. Chimera v. 1.15 on the same computer and notice that the publication presets for Chimera (Preset publication 1) look to my eye far superior to the preset publication setting for ChimeraX. This is really noticeable when comparing side by side at 400% enlargement. The attached tif file was created from powerpoint at 300 dpi comparing the same set of pdbs superimposed using Matchmaker from similar vantage points (but colored differently) and saved as tiff files or copied using screenshots. To my eye, the screenshot of the Chimera image is better than the ChimeraX tiff and the Chimera tiff is the best of all. The alpha helices in ChimeraX look washed out and the shading is less defined. Is there any way to get comparable images to the Chimera preset publication 1 in ChimeraX? Also, although these images are from the same pdb sources, it seems that the backbone ribbon is much more jagged in ChimeraX. Is there more smoothing in the algorithm for Chimera? Not that it matters that much, but I'd just like to know. Thanks, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu On Wed, Jan 5, 2022 at 12:13 PM Elaine Meng via Chimera-users < chimera-users(a)cgl.ucsf.edu> wrote: > You can remove hydrogens from the protein part only using Chimera (or > ChimeraX) command: > > delete H & protein > > That would not include the water, however. You could also do this to > remove water hydrogens: > > delete H & solvent > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Jan 5, 2022, at 12:50 AM, Enrico Martinez via Chimera-users < > chimera-users(a)cgl.ucsf.edu> wrote: > > [...] > > one question: > > how I could remove only protein's Hydrogen atoms using Chimera's > > command line (keeping them on the ligand)??? > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users >

5 11

Per-residue correlation coefficient
by Tom Goddard 10 Jan '22

10 Jan '22

Hi Yumeng, It would be useful if ChimeraX could report the per-residue correlation of an atomic model with a map as Phenix can do. I'll made a feature request for that https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5897 You can make feature requests yourself using ChimeraX menu entry Help / Report a Bug.... Bugs and feature requests go into our ChimeraX issue tracking database. There is a ChimeraX plugin called StrudelScore from the EMDB that gives per-residue fit statistics. You can get the plugin using ChimeraX menu Tools / More Tools.... There is online documentation here https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxstrudelscore <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxstrudelscore> and a tutorial https://ftp.ebi.ac.uk/pub/databases/emdb_vault/strudel_tutorials/introducti… <https://ftp.ebi.ac.uk/pub/databases/emdb_vault/strudel_tutorials/introducti…> Also there is a ChimeraX command resfit that lets you look at the fit of each residue in the density, moving a slider to go to the next residue. It can also make a video, here is an example, https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/images/resfit.mp4 <https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/images/resfit.mp4> https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html <https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html> and here is resfit command documentation https://www.cgl.ucsf.edu/chimerax/docs/user/commands/resfit.html Tom Example of resfit command display of residue fit to map. > On Jan 10, 2022, at 3:48 PM, Yumeng Yan <yumeng.yan(a)cpr.ku.dk> wrote: > > Hi Tom, > > Many thanks for your reply. It works follow your suggestion. I can not open ChimeraX in the gui mode while the ChimeraX is installed on a remote cluster and I did not configure it correctly, so bad. Another question, could you add the measure correlation with cc output for each residue in the structure like in Phenix? > > Best, > Yumeng > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Tuesday, January 11, 2022 12:38:42 AM > To: Yumeng Yan > Cc: chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> > Subject: Re: [chimerax-users] No cc when using fitmap > > You don't often get email from goddard(a)sonic.net <mailto:goddard@sonic.net>. Learn why this is important <http://aka.ms/LearnAboutSenderIdentification> > Hi Yumeng, > > I would not expect any difference in the correlation coefficient between Windows and Linux or with a large map versus a small map. > > First the command you listed does not do any fitting since you use "shift false rotate false" which does not allow the model to move. > > fitmap #2 inMap #1 resolution 4.0 metric correlation shift false rotate false > > So I assume you are doing this just to measure the correlation coefficient. And your output says the correlation coefficient is 0. That most likely means the atomic model is not located in the map. Why don't you just do the same steps in gui mode and see what happens -- it should produce exactly the same result as nogui mode. Also note that the displayed surface level matters because by default fitmap only uses data above the contour level of the displayed surface of the map you are fitting into. That actually may explain why your large map case did not work, because if you open a large map ChimeraX may initially just show a single plane in gray scale instead of a surface, and with no surface it won't have a surface level. So to get a predictable result you should use the volume command to show a surface of the full map and set the threshold level you want to use, for example, > > volume #1 style surface region all level 0.2 > > I see that ChimeraX does not have the "measure correlation" command that is in the older Chimera program. I will try to add that. > > Tom > > > > >> On Jan 10, 2022, at 2:14 PM, Yumeng Yan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Hi, >> >> When I tried to use fitmap function ChimeraX in Linux with --nogui option, I got no CC output when the Cryo-EM map is large(1.6GB) and I think in this situation, the local fit did not work. When the map was cut of a half size, it works. But it works well on Windows. Could you help me? >> >> Here are the commands: >> open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb >> fitmap #2 inMap #1 resolution 4.0 metric correlation shift false rotate false >> >> Here is the log information: >> INFO: >> UCSF ChimeraX version: 1.4.dev202201082018 (2022-01-08) >> INFO: >> © 2016-2021 Regents of the University of California. All rights reserved. >> INFO: >> Executing: open .33092SymAndFit.cxc >> INFO: >> Executing: open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 0% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 8% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 16% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 24% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 32% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 40% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 48% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 56% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 64% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 72% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 80% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 87% >> STATUS: >> Done reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc >> STATUS: >> Computing histogram for Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc >> STATUS: >> Computing Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292 >> STATUS: >> Calculated Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292, with 10911480 triangles >> INFO: >> Opened Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc as #1, grid size 750,750,750, pixel 1.1, shown at level 0.292, step 1, values float32 >> INFO: >> Chain information for fit_11.pdb #2 >> --- >> Chain | Description >> [F](cxcmd:select /F:2-219 "Select chain") | [No description >> available](cxcmd:sequence chain #2/F "Show sequence") >> >> >> INFO: >> Executing: fitmap #2 inMap #1 resolution 8.0 metric correlation shift false rotate false >> INFO: >> Opened fit_11.pdb map 8 as #3, grid size 40,42,43, pixel 2.67, shown at level 0.0533, step 1, values float32 >> INFO: >> Fit map fit_11.pdb map 8 in map Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc using 2211 points >> correlation = 0, correlation about mean = 0, overlap = 0 >> steps = 24, shift = 0, angle = 0 degrees >> >> INFO: >> Position of fit_11.pdb map 8 (#3) relative to Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc (#1) coordinates: >> Matrix rotation and translation >> 1.00000000 0.00000000 0.00000000 0.00000000 >> 0.00000000 1.00000000 0.00000000 0.00000000 >> 0.00000000 0.00000000 1.00000000 0.00000000 >> Axis 0.00000000 0.00000000 1.00000000 >> Axis point 0.00000000 0.00000000 0.00000000 >> Rotation angle (degrees) 0.00000000 >> Shift along axis 0.00000000 >> >> STATUS: >> 24 steps, shift 0, rotation 0 degrees, correlation 0.0000 >> >> >> Best wishes, >> Yumeng >> >> Yumeng Yan >> Postdoctoral Fellow >> >> Taylor and Rasmussen Group >> University of Copenhagen >> Faculty of Health and Medical Sciences >> Novo Nordisk Foundation Center for Protein Research >> >> Blegdamsvej 3B, building 6 >> 2200 Copenhagen N >> DENMARK >> >> yumeng.yan(a)cpr.ku.dk <mailto:yumeng.yan@cpr.ku.dk> >> >> <OutlookEmoji-1638361915486c0a23484-e68c-4b46-9d5a-75949bd8128d.png> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl…>

1 0

No cc when using fitmap
by Yumeng Yan 10 Jan '22

10 Jan '22

Hi, When I tried to use fitmap function ChimeraX in Linux with --nogui option, I got no CC output when the Cryo-EM map is large(1.6GB) and I think in this situation, the local fit did not work. When the map was cut of a half size, it works. But it works well on Windows. Could you help me? Here are the commands: open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb fitmap #2 inMap #1 resolution 4.0 metric correlation shift false rotate false Here is the log information: INFO: UCSF ChimeraX version: 1.4.dev202201082018 (2022-01-08) INFO: © 2016-2021 Regents of the University of California. All rights reserved. INFO: Executing: open .33092SymAndFit.cxc INFO: Executing: open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 0% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 8% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 16% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 24% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 32% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 40% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 48% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 56% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 64% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 72% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 80% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 87% STATUS: Done reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc STATUS: Computing histogram for Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc STATUS: Computing Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292 STATUS: Calculated Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292, with 10911480 triangles INFO: Opened Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc as #1, grid size 750,750,750, pixel 1.1, shown at level 0.292, step 1, values float32 INFO: Chain information for fit_11.pdb #2 --- Chain | Description [F](cxcmd:select /F:2-219 "Select chain") | [No description available](cxcmd:sequence chain #2/F "Show sequence") INFO: Executing: fitmap #2 inMap #1 resolution 8.0 metric correlation shift false rotate false INFO: Opened fit_11.pdb map 8 as #3, grid size 40,42,43, pixel 2.67, shown at level 0.0533, step 1, values float32 INFO: Fit map fit_11.pdb map 8 in map Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc using 2211 points correlation = 0, correlation about mean = 0, overlap = 0 steps = 24, shift = 0, angle = 0 degrees INFO: Position of fit_11.pdb map 8 (#3) relative to Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 Axis 0.00000000 0.00000000 1.00000000 Axis point 0.00000000 0.00000000 0.00000000 Rotation angle (degrees) 0.00000000 Shift along axis 0.00000000 STATUS: 24 steps, shift 0, rotation 0 degrees, correlation 0.0000 Best wishes, Yumeng Yumeng Yan Postdoctoral Fellow Taylor and Rasmussen Group University of Copenhagen Faculty of Health and Medical Sciences Novo Nordisk Foundation Center for Protein Research Blegdamsvej 3B, building 6 2200 Copenhagen N DENMARK yumeng.yan(a)cpr.ku.dk<mailto:yumeng.yan@cpr.ku.dk> [1638361915486]

2 2

Blob measurement question?
by Noriega, Heather 10 Jan '22

10 Jan '22

Hello, I hope you all are well and had a lovely holiday. I have a couple questions. I was able to measure the inner volumes through the directions Tom had given me a couple months ago: open 1lp3 open alphafold prediction matchmaker #2 to #1 sym #2 symmetry #1 copies true molmap #3 12 volume #4 level 0.07 choose "blob", right click to color it surface splitbycolor #4.1 view position #5 sameAs #4 hide #4,5.1 model measure volume #5.2 For some reason, on one of my AAVs it is giving me a different volume that is not accurate. The AAV3B inner volumes seems correct since the sequence for VP4 is shorter, therefore has more space in the inside: AAV3B VP3 only: 2.348 X 10^6 AAV3B VP4 only: 2.488 x 10^6 However, the AAV8 is showing the opposite with VP4 having less space compared to VP3, and the sequences are very similar between AAV3B and AAV8. I am hoping you may know why? or was curious if this may be a bug? And how can I fix it to reflect the data given to me? AAV8 VP3: 2.558 x 10^6 AAV8 VP4: 2.478 x 10^6 I also attached an MSA to help show that the sequences are very similar length wise, so they should come out to be close in inner volume measurements. Last question, I am still learning but is there a way to use the Chimera and ChimeraX through a command prompt with the computer or is the command line the only thing available? I thought maybe I could try to see where the error is coming from using a prompt, but I do not know how to access this. Thank you, and I hope to hear from you soon. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

2 3

Volume Render settings
by Kelvin Lau 10 Jan '22

10 Jan '22

Hello I was wondering if there is in the future a volume settings function such as that in Chimera in a tool GUI. I am referring to such things such as the Surface and Mesh options which are easily accessible via the GUI in Chimera for things like surface smoothing, subdivision, smoothing etc. I have found a workaround with commands however in this case a GUI implementation is quite useful as one can easily click and see different visualisations. Best regards Kelvin -- Kelvin Lau http://about.me/kelvin.lau kelvin.kclau(a)gmail.com

2 1

Re: [chimerax-users] swapnaa not working in Chimerax
by Elaine Meng 07 Jan '22

07 Jan '22

On Jan 7, 2022, at 9:15 AM, Antón Vila-Sanjurjo <anton.vila(a)udc.es> wrote: > > Hi Elaine, > everytime I try the swapnaa command in ChimeraX I get an error because the command is not recognized. Has swapna being implemented in ChimeraX? > best, > Antón Hi Antón, ChimeraX does not have a "swapna" command currently, although it does have "swapaa". You can see the list of commands using menu: Help... User Guide. There is also a copy of the ChimeraX User Guide at our website, but it may be newer than the version of the program that you have downloaded: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html> In the meanwhile, you can use Chimera for "swapna" and save a PDB file, then read it into ChimeraX if you want. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Nucleotide styles
by Derek Harris 05 Jan '22

05 Jan '22

Hello, I am working on a figure in ChimeraX. None of the nucleotide styles seem to be working for me, whether inputted from the button command on the menu bar or from the command line. The log indicates the command is accepted without error, but there is no visual change to the model. Derek F. Harris Senior Researcher Seefeldt Lab<http://www.seefeldtlab.org/> Department of Chemistry and Biochemistry Utah State University 435.797.7392

2 1

Question on Interactive H-Bond Histogram
by Bing Xu 05 Jan '22

05 Jan '22

Dear ChimeraX staff, I am sorry to bother you. I used ChimeraX to analyze the two protein complexes. I followed the guide for interactive H-Bond Histogram, but I still can not get the interaction amino acid of two proteins like the examples in ChimeraX Web [cid:image001.png@01D80242.867E4970] I am wondering whether you can provide me with more detailed guide for H-Bond histogram function. I do appreciate your help. Best, Bing Xu Research associate Bing(a)mmrl.edu<mailto:Bing@mmrl.edu> Masonic Medical Research Institute Lab: 315-624-7481 / Fax: 315-735-5648 2150 Bleecker Street | Utica, NY 13501 www.mmrl.edu<http://www.mmrl.edu/> [Primary Logo]

2 1

problem on Protein complex prediction
by Bing Xu 31 Dec '21

31 Dec '21

Dear ChimeraX Staff, I tried to used ChimeraX to predict to two proteins complex. After Alfafold Run finished, I can't find the result. Alfafold Run window showed that the prediction was completed. I attached the pictures of Alfafold Run window. Could you please help me to figure out what is wrong with ChimeraX? I do appreciate your help. Thanks and Happy New Year! Bing

2 1

focus and set pivot functions
by Antón Vila-Sanjurjo 30 Dec '21

30 Dec '21

Hello, I have used the old Chimera quite a bit and I'm trying to get used to ChimeraX. There are a couple of tools that I found very useful in the old chimera: "focus" and "set pivot". Both were under the "Actions" menu and, with large structures like the ribosome, these two tools allowed me to quickly inspect any residues that were selected with any other tools. "Focus" is not there anymore and while "set pivot" is, it doesn´t seem to work as it used to. I wonder if these tools, in their old flavors, are still available in ChimeraX. best, Antón -- Antón Vila-Sanjurjo, PhD Profesor del Area de Genética Departamento de Bioloxía Facultade de Ciencias Universidade da Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2267 e-mail: anton.vila(a)udc.es

2 8

ChimeraX for complex prediction
by Bing Xu 29 Dec '21

29 Dec '21

Hello Chimerax staff, I used ChimeraX to predict the complex of two proteins. After Alfafold Run finished, the Alfafold Run window is dark, I can not find any result. I tried to run the same two proteins again, it showed the following information. [Graphical user interface, text, application, email Description automatically generated] I am wondering what wrong with these predication. Thanks, Bing

2 1

Question on result
by Bing Xu 29 Dec '21

29 Dec '21

Hello, I used chimerax to predict interaction of two proteins. After load the two protein sequencing and run Alfold prediction, I can not find the result. I check the download fold and there is no Chimerax in the fold. I am wondering how I can find my prediction results I do appreciate your help. Thanks, Bing Xu

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Re: [chimerax-users] [Chimera-users] Move models around independent of each other in Chimera X
by Elaine Meng 24 Dec '21

24 Dec '21

HI Prathvi, Glad you like drag-and-drop! There is a chimerax-users(a)cgl.ucsf.edu address for ChimeraX questions, which I've CC'd here. (1) Yes you can move models selectively with the mouse, but it is different in ChimeraX than in Chimera. In ChimeraX, there are different "mouse modes", meaning what happens when you use some mouse button or touchpad to click and drag. There are mouse modes to move only the model(s) with some part selected, or only the model you just clicked on. You can assign the right mouse button (or its touchpad equivalent) by clicking an icon in the Right Mouse toolbar of icons across the top, or you can use the “mousemode” command to assign the modes to any button or scroll wheel. See Right Mouse toolbar documentation with pictures of the icons and what they mean: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> ... and mousemode command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> For example, for moving things manually (with the mouse or touchpad motions) you would want to use the “translate selected model” and “rotate selected model” mouse modes. Selection in ChimeraX is similar to that in Chimera: <https://rbvi.ucsf.edu/chimerax/docs/user/selection.html> (1a) you can also move models selectively with ChimeraX commands like "turn" "move" etc. by using their "models" options. (2) depth-cueing is a option of the ChimeraX lighting command. E.g. command: lighting depthCue false lighting command and its options <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 23, 2021, at 11:42 PM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > > First of all, thank a million to the chimera X development team for incorporating the drag & drop feature in chimera X. I really missed it in chimera. > > However, after opening two models in the same window, I am unable to find a way to move/rotate model-1 in such a way that it does not move/rotate model-2. I could do this in chimera by unchecking the box for model-2 but when I do the same in chimera-X, it doesn't seem to work. > > Also, I am unable to find a way to disable depth cueing in chimera X. Please help. > > Thank you > > -- > Prathvi Singh, > Research Fellow, > Department of Biological Sciences & Bioengineering, > Indian Institute of Technology, Kanpur-208016 > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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The problem of ligands disappearing when the file is converted
by Kenji MATSUI 20 Dec '21

20 Dec '21

Dear ChimeraX Thank you very much for your kind words in the past. When I opened the PDB file and mol2 file saved by pymol using the method you gave me, the ligands disappeared. How can I get pymol to display the ligands as well? Here is in detail. As you suggested, I created a new model by combining #1 and #10, and saved the newly single model in a PDB file. However, when I displayed this file in pymol, I could not see the ligand as shown in the figure. [image: image.png] [image: image.png] So we tried to align the ligand OSW-1 to the protein osh4 in this figure, but it was difficult to analyze because OSW-1 was far away from the distance of the protein osh4 as shown in the figure below. [image: image.png] Refernece：Save command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> Also, I've looked at tutorials and other sites on the Internet to try to figure out what's causing this, but no luck! I'm sorry for the many questions. --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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Re: [chimerax-users] [Chimera-users] .dae export for ChimeraX
by Tom Goddard 18 Dec '21

18 Dec '21

Hi Byrne, Thanks for the info about exporting models for iOS. Glad you found a way to export a virus model from ChimeraX suitable for use in iOS apps made with Xcode. The STL format is just a list of triangles, each with 3 vertex (x,y,z) coordinates, used mostly for 3D printing. It does not have vertex normal vectors which are used to give smoother lighting. In the future maybe ChimeraX will directly export Collada (*.dae) files and you will be able to export a usable model without running it through Blender. As I mentioned before we support GLTF but not Collada currently. Our ChimeraX efforts are mostly to help researchers analyze molecular structures so adding this does not have highest priority. Unfortunately there are hundreds of feature requests we do not have time to implement with our limited funding. Tom > On Dec 18, 2021, at 9:34 AM, Byrne Pedit <bpedit(a)comcast.net> wrote: > > Hello again Tom, > > A follow-up follow-up. After extensive testing I have found a useable workflow from ChimeraX to iOS. Of course iOS apps may utilize PDB viewers, this is for folks who may want to incorporate models, in customized ways, into SceneKit for manipulation. > > ChimeraX ––> STL ––(graphics editor)––> DAE ––Xcode––> SCN > > • In Chimera > – reduce polys as much as possible* > – export individual elements, e.g. chains, if you want individual control (materials, etc) > • In a graphics editor: > – eliminate polygonal faceting of STL files > - Blender, check Auto Smooth in addition to toggling on Smooth Shading > - Cinema 4D, add a phong tag > – recenter if desired, add additional elements > > *You might want to add surfaces to your reducing file-size tutorial. In the model below, the spike's resolution was set to 7, gridSpacing 3. You also need to click Hide for Atoms and Cartoons; otherwise they will severely bloat the file even though not seen. The entire file size of this SARS-CoV-2 model, as used by iOS, is 1.2 Mb (all but one of the spikes are all clones). > > Thanks again for the help, > > Byrne > > > > > > >> On Dec 3, 2021, at 11:00 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Byrne, >> >> Thanks! So Blender can convert GLTF to Collada. The ChimeraX GLTF is binary and Collada is all text, so no surprise that the file size is much larger. If we add Collada support it would be produced directly from the ChimeraX scene, not converting from GLTF. But we have hundreds of new feature requests so I don't think Collada output is likely to be added soon, unless a funded project needs it. >> >> Tom >> >>> On Dec 3, 2021, at 9:48 AM, Byrne Pedit <bpedit(a)comcast.net <mailto:bpedit@comcast.net>> wrote: >>> >>> Hi Tom, >>> >>> A follow-up for future reference. Blender, the one recommendation I found on StackOverflow, is indeed capable of converting GLTF to DAE. But the conversion bloats the files by as much as 10x! In addition, the hierarchy is only partially preserved. I tried an on-line converter with even less satisfactory results. So I think this pathway is a bust. This might serve as a fair warning for ChimeraX developers to avoid an internal conversion from GLTF if introducing a DAE export option. >>> >>> >>> Byrne >>> >>> >>> >>> >>>> On Dec 2, 2021, at 2:22 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>> >>>> Hi Byrne, >>>> >>>> I agree, OBJ and STL are very limited compared to Collada and GLTF. OBJ is supported by almost every 3D model program and STL is commonly used for 3D printing (single color) which is why they are in ChimeraX. GLTF is definitely the best option in ChimeraX for your case. >>>> >>>> There appear to be lots of programs that convert GLTF to Collada and the other direction too. But I have not tried any of them so don't have any recommendation. Let us know if you find one that works well -- other ChimeraX users may have the same need. >>>> >>>> A major stumbling block exporting 3D models from ChimeraX (or Chimera) is that they use vertex colors, while most of the non-biology 3D model world uses texture colors, and will simply ignore vertex colors losing all your color information. That example I linked to in the last email describes a relatively new ChimeraX feature to export texture colors (for limited cases, e.g. discrete colors only). >>>> >>>> Another common problem exporting molecular models for use in other software is that the file size and number of triangles is too large for the application that you want to use them in, often tens of millions of triangles or hundreds of Mbytes to Gbytes in size. The example also shows how to tell ChimeraX to limit the number of triangles. >>>> >>>> https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html <https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html> >>>> >>>> Tom >>>> >>>> Model from gltf export from linked ChimeraX example >>>> >>>> <spike.png> >>>> >>>> >>>>> On Dec 2, 2021, at 2:04 PM, Byrne Pedit <bpedit(a)comcast.net <mailto:bpedit@comcast.net>> wrote: >>>>> >>>>> Hello Tom, >>>>> >>>>> Thanks for the response. I tried the GLTF export, not recognizable by Xcode (the development platform for iOS and Mac OS). The only ChimeraX file options I’ve found to be openable are OBJ and STL. These are, however, problematic and unusable. >>>>> >>>>> But your hint of using GLTF as an intermediary offers an avenue for exploration, it’s not a format I’ve used. I see it supports scene graph hierarchy, absent with OBJ and STL( exported from ChimeraX anyway) so this is promising. Now to find a converter. >>>>> >>>>> The GLTF export link is informative, it may help further refine my approach. Interestingly, the molecule you’ve chosen for demo purposes appears to be the one, or a variant thereof, I’ve been testing with! >>>>> >>>>> Thanks again, >>>>> >>>>> Byrne >>>>> >>>>> >>>>>> On Dec 2, 2021, at 12:30 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>>>> >>>>>> Hi Byrne, >>>>>> >>>>>> We have long been interested in adding Collada format export of scenes from ChimeraX. Here is the feature request for that >>>>>> >>>>>> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485> >>>>>> >>>>>> But our scene export in ChimeraX has focused on GLTF format, as that has been the most requested. Here is an example showing GLTF export from ChimeraX (including texture colors). >>>>>> >>>>>> https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html <https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html> >>>>>> >>>>>> ChimeraX also exports OBJ, STL, X3D, VTK as shown in the save command docs >>>>>> >>>>>> https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats> >>>>>> >>>>>> Can you make use of GLTF files? If not, a quick solution might be to convert ChimeraX GLTF files to Collada with third-party software. >>>>>> >>>>>> Tom >>>>>> >>>>>>> On Dec 2, 2021, at 10:41 AM, Byrne Pedit via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >>>>>>> >>>>>>> ChimeraX is awesome and definitely superior to the original but for the inability to export as .dae (Collada). Is that possibly on the to-do list? This is important for those of us (just me?) writing interactive molecular apps for devices. It is the only satisfactory path I’ve found between a PDB file and SCNNodes/Scenes in iOS. (See the iOS app ‘BioMole’, free, if interested in an application.) >>>>>>> _______________________________________________ >>>>>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>>>>> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> >>>>>>> >>>>>> >>>>> >>>> >>> >> >

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Fwd: Question: PDB file creation
by Elaine Meng 17 Dec '21

17 Dec '21

> Begin forwarded message: > > From: Kenji MATSUI <s214903z(a)st.go.tuat.ac.jp> > Subject: Question: PDB file creation > Date: December 16, 2021 at 7:20:41 PM PST > Cc: Kaori Sakurai <sakuraik(a)cc.tuat.ac.jp> > > Dear UCSF ChimeraX > > Thank you for allowing me to use your software. I am Japanese, so I hope you will understand that there are some inappropriate expressions. I would like to ask you two questions. > > First, I would like to know how to convert a cxs file saved in Chimera X to a PDB file. > > Aim > To display the interaction between a protein (osh4) and a ligand (OSW-1) in pymol > > Methods I have tried > I found a way to convert mmCIF to PDB file, but I could not find a site to convert cxs file to PDB file. > > Second, How to deal with the following error that appears when the structure of the osh4-OSW-1 complex is shown. > > APBS electron > Error: The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electron density. > Thank you for your cooperation. > --------------------------------------------------------------------------- > Kenji Matsui > Graduate School of Tokyo University of Agriculture and Technology > 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan > Mail: s214903z(a)st.go.tuat.ac.jp <mailto:s214903z@st.go.tuat.ac.jp> Hi Kenji, I omitted your cxs file from this message since I thought maybe you wanted to keep it private (messages on this chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> mailing list can be seen by the public). I didn't see that APBS error when I opened the cxs file in ChimeraX. It appears to be a message from another program (not ChimeraX): the APBS program, which calculates electrostatic potential. The error is exactly what it says: some residues in the structure are missing some atoms, which would affect the calculation of electrostatic potential values. Short answer #1 is why not look at the interactions in ChimeraX instead of Pymol? You can calculate H-bonds, find contacts, etc. See this tutorial, for example <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html>> Short answer #2 is that you can open the session (cxs) file in ChimeraX and then save a PDB file with the "save" command or the menu: File... Save... (choose Files of type: PDB). HOWEVER, a longer answer may be required here because I can see from opening your cxs file that it contains many models, I guess a receptor (model #1) and ligands from docking (models #2-258) with only some ligands displayed (models #10-17). I'm guessing you want to save only the ones that are displayed. You could save models #1,10-17 into one multi-model PDB, file but probably for analysis in Pymol or other programs, you would instead need to combine each ligand with receptor and save it separately. In other words, you may need to make a new model by combining #1 with #10, and then save the new single model to a PDB file. For example: combine #1,10 modelId #300 save /Users/meng/Desktop/result10.pdb models #300 relModel #1 Then repeat for other ligands, combining #1 with #11 to make a new model and saving that new model, combining #1 with #12, etc. See the help links below for the options of each command. Save command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>> Combine command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Color docking resulls by rank
by Visvaldas K. 17 Dec '21

17 Dec '21

Dear Users and Developers, I have a ViewdockX question (but I guess it's a more generic one, about coloring models/submodels): is there a trick to color docking results by rank, like rank was some sort of B-factor? Or even by docking energy (score), but that's maybe too much. I could color each "submodel" by hand, but I don't know how to obtain color gradients, say distributed at even distances between blue and red. Years ago I was able to do similar trick in Chimera, but I completely forgot how I did that :( Thank you, Vis On Friday, December 17, 2021, 05:24:30 PM GMT, chimerax-users-request(a)cgl.ucsf.edu <chimerax-users-request(a)cgl.ucsf.edu> wrote: Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users or, via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..." Today's Topics: 1. independent centers of rotation (Elaine Meng) 2. Change the directory for data fetched from databases (Guillaume Gaullier) 3. Re: Change the directory for data fetched from databases (Tom Goddard) 4. Re: Change the directory for data fetched from databases (Guillaume Gaullier) 5. Re: Change the directory for data fetched from databases (Tristan Croll) 6. Re: Change the directory for data fetched from databases (Guillaume Gaullier) 7. PDB: 7OVR (Veler, Hana (NIH/NCI) [F]) 8. Re: PDB: 7OVR (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Dec 2021 12:51:58 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Abigail Jackson <ajackson(a)scripps.edu> Cc: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] independent centers of rotation Message-ID: <90DEEA37-1BF5-4F52-AF35-DF81F0B4F273(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi Abigail, Ah, you're referring to the "independent centers of rotation" mode in Chimera. By default, the "tile" command in Chimera automatically turns it on. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/tile.html> I agree that this mode is very useful, but unfortunately it does not yet exist in ChimeraX. It is listed in the missing features section of the ChimeraX download page. <https://www.rbvi.ucsf.edu/chimerax/download.html> Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 15, 2021, at 12:28 PM, Abigail Jackson via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi there, > I have a question regarding the tile function in ChimeraX. In the original Chimera, once multiple maps were tiled they would all rotate individually and the grid itself was fixed in space. In ChimeraX, however, once maps are tiled the entire grid rotates as a unit and the individual maps are fixed. Do you know if there is an option to have the maps spin individually instead, like in the original Chimera? > > Hopefully that description makes sense. Thank you in advance for your help! > Best, > Abigail Jackson > The Scripps Research Institute ------------------------------ Message: 2 Date: Thu, 16 Dec 2021 10:08:26 +0000 From: Guillaume Gaullier <guillaume.gaullier(a)icm.uu.se> To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] Change the directory for data fetched from databases Message-ID: <7B64261E-92A8-45FF-BF14-0B597E14A98B(a)icm.uu.se> Content-Type: text/plain; charset="utf-8" Hello, The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn?t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands). The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX). Thank you, Guillaume N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ------------------------------ Message: 3 Date: Thu, 16 Dec 2021 14:50:25 -0800 From: Tom Goddard <goddard(a)sonic.net> To: Guillaume Gaullier <guillaume.gaullier(a)icm.uu.se> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] Change the directory for data fetched from databases Message-ID: <8D292E49-13E7-4DF0-9B94-7EAC424DA7D0(a)sonic.net> Content-Type: text/plain; charset=utf-8 Hi Guillaume, There is no setting to change the location where ChimeraX caches fetched files. It is always ~/Downloads/ChimeraX On a multi-user workstation is the idea that every person would change the ChimeraX setting to point to a common cache directory? Will people cooperate with that? Each person of course has their own ChimeraX settings. Everyone will also need write access to that directory. There are no site-wide settings in ChimeraX. You could modify the ChimeraX application file, a file in the distribution (here's the path for Linux) chimerax/lib/python3.9/site-packages/chimerax/core/fetch.py making _cache_dirs = ['/usr/local/chimerax_fetch'] near the top would I think change to use that directory. Of course each time you install a new ChimeraX it would need such a change, and if individual users install their own ChimeraX version it will use ~/Downloads/ChimeraX. Tom > On Dec 16, 2021, at 2:08 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hello, > > The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn?t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands). > > The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX). > > Thank you, > > Guillaume > > > > > > > > > > N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > ------------------------------ Message: 4 Date: Fri, 17 Dec 2021 08:40:06 +0000 From: Guillaume Gaullier <guillaume.gaullier(a)icm.uu.se> To: Tom Goddard <goddard(a)sonic.net> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] Change the directory for data fetched from databases Message-ID: <ED531B0A-5F66-4E86-920E-565966A5D8A3(a)icm.uu.se> Content-Type: text/plain; charset="utf-8" Hi Tom, This is the use case I had in mind indeed. Model files are small enough that duplication doesn?t matter, but a shared cache for maps could be convenient. I was simply asking in case there was a supported way to achieve this that I had missed in the documentation, but I can absolutely live with the current default. Thank you for your answer. Cheers, Guillaume On 16 Dec 2021, at 23:50, Tom Goddard <goddard(a)sonic.net<mailto:goddard@sonic.net>> wrote: Hi Guillaume, There is no setting to change the location where ChimeraX caches fetched files. It is always ~/Downloads/ChimeraX On a multi-user workstation is the idea that every person would change the ChimeraX setting to point to a common cache directory? Will people cooperate with that? Each person of course has their own ChimeraX settings. Everyone will also need write access to that directory. There are no site-wide settings in ChimeraX. You could modify the ChimeraX application file, a file in the distribution (here's the path for Linux) chimerax/lib/python3.9/site-packages/chimerax/core/fetch.py making _cache_dirs = ['/usr/local/chimerax_fetch'] near the top would I think change to use that directory. Of course each time you install a new ChimeraX it would need such a change, and if individual users install their own ChimeraX version it will use ~/Downloads/ChimeraX. Tom On Dec 16, 2021, at 2:08 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hello, The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn?t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands). The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX). Thank you, Guillaume N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

2 1

PDB: 7OVR
by Veler, Hana (NIH/NCI) [F] 17 Dec '21

17 Dec '21

To whom it may concern, The command “show sel atoms’ does not work in the 7OVR structure and I was wondering how can I fix this? I wanted to show certain residues as atoms in the structure. When I open other structures, e.g. 5FMM, the command works perfectly fine. Would you know what could be the cause? Thanks, Hana

2 6

Change the directory for data fetched from databases
by Guillaume Gaullier 17 Dec '21

17 Dec '21

Hello, The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn’t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands). The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX). Thank you, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

3 4

ChimeraX Question
by Abigail Jackson 15 Dec '21

15 Dec '21

Hi there, I have a question regarding the tile function in ChimeraX. In the original Chimera, once multiple maps were tiled they would all rotate individually and the grid itself was fixed in space. In ChimeraX, however, once maps are tiled the entire grid rotates as a unit and the individual maps are fixed. Do you know if there is an option to have the maps spin individually instead, like in the original Chimera? Hopefully that description makes sense. Thank you in advance for your help! Best, Abigail Jackson The Scripps Research Institute

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Fwd: ChimeraX VR question or suggestions
by Elaine Meng 14 Dec '21

14 Dec '21

> > From: Alejandro Villalta Cásares <alejandrovillaltac(a)gmail.com> > Subject: ChimeraX VR question or suggestions > Date: December 13, 2021 at 4:36:03 AM PST > To: chimerax(a)cgl.ucsf.edu > > Dear ChimeraX staff, > > I tested the ChimeraX VR mode today. I was very happy on how it looks and how easy it was to move and see some parts of the structure compared to the flat screen version. Nevertheless, the function that I think it will very useful the VR is to segment and select different segments to save them later. That I couldn't manage to do it after some time I managed to be able to select one region but no more than one at time. It should be nice to add the ability to select multiple regions or at least as in the flat screen that it tells you the name of the models that you are pointing, like that we could pass through command lines. Also it should be nice that a keyboard appears on the headset in order to type on the command lines, but it is true that is a minor point, if it can be written directly on the PC. > > Thank you very much for this amazing function, > > I hope that this constructive mail could help you to improve it more. > > Sincerely yours, > > Alejandro Villalta >

3 3

Analog command to reinit & create?
by Eric Pettersen 13 Dec '21

13 Dec '21

> Begin forwarded message: > > From: "Jan Gebauer" <jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de>> > Subject: Analog command to reinit & create? > Date: December 13, 2021 at 7:11:40 AM PST > To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> > Reply-To: "Jan Gebauer" <jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de>> > > > Hi everyone, > > I am currently teaching a crystallographic course and this year I am introducing ChimeraX for the first time (previous years we have used PyMol). > I still am in the middle of my personal transiston from PyMol to ChimeraX and potentially I am still stuck too much in the "PyMol"-way to do it, but I still miss a couple of commands. Could anyone help with that? > > 1) Analog to Reinit > I generate all my publication figures with scripts (now cxc). The Reinit command in Pymol, always gave me a fresh enviroment, however the closest analog I found "Close" only closes the current model. All other settings (Lightning etc.) are kept and only reset after closing ChimeraX. Therefore, I do not get the same results from my script, if I run it multiple times... > > 2) Create object > Is there a way to copy a selection of atoms into a new molecule - for complicated visualisations? > > Thanks so far to the developers - I love more things on ChimeraX than I miss 👍 > Best, > Jan > > -- > Dr. Jan Gebauer > AG Baumann / Biochemistry Cologne > Zülpicher Str. 47 / 50764 Köln > +49 - 221 - 470 - 3212

3 2

ViewDockX for Autodock Vina error
by Visvaldas K. 13 Dec '21

13 Dec '21

Dear colleagues, for some reason ChimeraX does not recognize pdbqt from Autodock Vina 1.1.2 as a "docking file", even though it opens pdbqt file just fine (The message: No suitable models found for ViewDockX). The documentation says that Autodock Vina is supported. Perhaps it's the version of Vina (I use 1.1.2, or preferably its fork Smina, while the newest version is 1.2)? If I knew what the file that ChimeraX recognizes as a "model" looks like, I'd write a script to reformat my pdbqt, but at the moment I'm in the dark... Not too bad since I still can view the structures, but perhaps I'm missing some cool features... Thank you in advance, Vis

3 2

Save ribbons and surfaces with minimal amount of vertices/faces
by Sarah Piper 13 Dec '21

13 Dec '21

Hi ChimeraX team and others, I got a bit of an unusual question and am interested to see whether it is possible! I am trying to use a short helix in ribbon style from ChimeraX into Blender, and use it to create a 'skeleton' for animations. For this, it would be most useful to have as few vertices as possible for the helix (basically only the 'invisible' coordinates themselves as 'line', instead of having it as a 3D view/thick helix. When I export a helix even with a very thin ribbon style through the command line (e.g. width and thickness to 0.1), this is unfortunately still too thick and creates too many vertices/faces. Setting these values to 0 gives errors. I have looked at the ribbon style editor in Chimera as well, and unfortunately the minimum settings are 0.05. Would it be possible to somehow set any of these parameters to 0 and save this as a file format suitable for 3D softwares (e.g. .glb)? Would it work through a python script potentially? (I'm not familiar with python in chimera yet but happy to learn more about this). And if so, would this be also applicable for surfaces, to reduce the numbers of vertices/faces that are exported? On another note, I was wondering whether it would be possible to set the chimaera scene 'world origin' to a particular coordinate set; I think in Pymol this is possible with resetting the camera view: cmd.set_view([ 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 40.0, 100.0, -20.0]) Sorry for these unusual question but looking forward to hearing back from anyone who might have any suggestions! Cheers, Sarah

3 4

Showing long coiled coil alpha helices as tubes
by Huiskonen, Juha T 13 Dec '21

13 Dec '21

Hi all, I am trying to render two long alpha helices forming a coiled coil as tubes instead of ribbons. The tubes rendered with default settings do not however follow the paths of the helices. Instead, the tubes become almost straight. Any suggestions? Best wishes, Juha

3 2

rotation parameters of the map
by Dmitry Semchonok 13 Dec '21

13 Dec '21

Dear colleagues, When I align one map to the other (either manually or by using the Fit option), I would like to know the applied rotation parameters. How to find them our when a) using just Fit option b) rotation manually and then using the Fit option? Thank you Sincerely, Dmitry

2 2

Question about chimeraX installization.
by 박시훈 11 Dec '21

11 Dec '21

Dear chimeraX users, I want to change the installation folder of chimeaX in linux (centos7.0). The default folder is user/bin however, I want to install chemeraX in the other folder because of my computer environments (the Master and Slave nodes do not share the usr/bin folder). Can I know how to change the installation folder? Best regards Si Hoon Park

2 1

1.3 release
by Eric Pettersen 10 Dec '21

10 Dec '21

UCSF ChimeraX version 1.3 has been released! Updates since version 1.2 (May 2021) include: - AlphaFold tool and command to get AI-predicted protein structures - Selection Inspector to inspect/change attributes of atoms, bonds, etc. - Scale Bar tool and command - new BLAST Protein GUI with easier controls for showing hit info such as source species, crystallographic resolution, ligands in structure - Altloc Explorer tool and command to switch among alternate locations - model loops and missing segments with Modeller - combine or copy models - change bond lengths - apply command files iteratively to multiple input files - list multiple map-fitting solutions from global search For more details, see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> Enjoy! --Eric

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re-sampled map (volume resample #X onGrid #Y) difference with general mrc map
by Dmitry Semchonok 10 Dec '21

10 Dec '21

Dear colleagues, I have an issue with the output map re-sampled from the resampling step protocol. Could you please explain how different the re-sampled map is compared to the general mrc map (without rotation manipulations)? Because it seems that some important information is missing or/changed in the re-sampled.mrc Kind regards, Dmitry

2 1

Re: [chimerax-users] alphafold predict multiuser syntax
by Tom Goddard 09 Dec '21

09 Dec '21

Hi Jerry, It is unlikely you will be able to get AlphaFold to predict multimers composed of multiple 1000 amino acid proteins even with the most powerful GPUs available. The EBI AlphaFold database produced by Google predicted structures of up to 2700 amino acids. From the paper that was done by combining the memory of 4 GPUs (which cannot be done on Colab), that might be 64 Gbytes. The GPU memory use of AlphaFold is said to be quadratic in number of residues. When I last tested with Google Colab GPUs with 16 Gbytes a few months ago it failed with 1000 amino acids. But that was AlphaFold 2.0 and now we are using AlphaFold 2.1. It would require testing, but it is very likely that 1500 total amino acids in a complex will run out of memory, and quite possibly 1000 will run out of memory when your GPU has only 16 Gbytes. This is one of the limitations of AlphaFold, and of the old Google Colab GPUs with only 16 Gbytes. The AlphaFold database has predictions for human proteins larger than 2700 amino acids made by breaking into 1400 amino acid chunks and computed at intervals of 200 amino acids. Then you can attempt to piece together those chunks. I give an example of that piecing together in ChimeraX here https://rbvi.github.io/chimerax-recipes/big_alphafold/bigalpha.html Tom > On Dec 9, 2021, at 10:12 AM, Jerry Honts <jerry.honts(a)drake.edu> wrote: > > Unfortunately several of the proteins I’m studying are ~1000 amino acids and the evidence is they form multimers. So I was wondering if Colab Pro + would actually succeed, or whether this is currently not a feasible solution. > > I should mention that I have students use Chimera in several of my courses to solve problems (and they like it), and I hope to move students to ChimeraX this year. So thanks for maintaining and refining this wonderful software. > > Jerry

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Re: [chimerax-users] alphafold predict multiuser syntax
by Tom Goddard 09 Dec '21

09 Dec '21

Hi Jerry, I have not tried Colab Pro+ which is $50 per month and claims to give faster GPUs, more memory, longer session times. I use Colab Pro which is $10 per month because the free Colab was sometimes not letting me run jobs more than 2 hours per day. https://colab.research.google.com/signup The main factor for running larger predictions (e.g. > 1000 amino acids) is GPU memory. With Colab Pro Google never gave me a GPU with more than 16 GBytes -- I get old Nvidia T4, P100 and K80 GPUs just like with free Colab. At UCSF I can run AlphaFold (not in ChimeraX) using new Nvidia A40 or A100 GPUs which have 48, 40 or 80 GBytes but I have not tested on large proteins to see how large. The runs on 800 amino acid predictions are about 2 to 3 times faster on these new GPUs. Tom > On Dec 9, 2021, at 9:44 AM, Jerry Honts <jerry.honts(a)drake.edu> wrote: > > Hi Tom: > > Many thanks for your quick reply! I so appreciate AlphaFold access being built into ChimeraX—it has already resulted in several interesting leads. > > As a second question if I may ask: would upgrading the Google Collab Pro + help with AlphaFold predictions? Any experience with this? > > Jerry

1 0

alphafold predict multiuser syntax
by Jerry Honts 09 Dec '21

09 Dec '21

I am trying to use the AlphaFold predict multimer function in ChimeraX 1.3 with this syntax like (comma-separated pasted sequences): alphafold predict MPEHPIQLASSNQVVSQILTTTQGSPTRQSKTFVYRSE,MSESPIRSSQYGKHVVNVSHIEKGQAPIYVSQSTVQNPIYVEKIVKVESSNT But I keep getting an error: Missing or invalid "sequence" argument: Sequences argument "MPEHPIQLASSNQVVSQILTTTQGSPTRQSKTFVYRSE,MSESPIRSSQYGKHVVNVSHIEKGQAPIYVSQSTVQNPIYVEKIVKVESSNT” is not a chain specifier, alignment id, UniProt id, or sequence characters I think I am following the syntax given in the online help file, but can you suggest a reason for this error? Single chain predictions have been working fine with pasted sequences. Thanks, Jerry E. Honts Drake University

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Re: [chimerax-users] Regarding animation Tool bar
by Elaine Meng 06 Dec '21

06 Dec '21

Hi Dilip, Sorry, only Chimera (not ChimeraX) has the Animation graphical interface currently. Of course, you can make movies with ChimeraX, but you would need to use a ChimeraX command script to do it. More information about making movies in ChimeraX, including links to tutorials with examples: <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 5, 2021, at 1:57 PM, Dilip Badgujar <dilip.badgujar(a)kemi.uu.se> wrote: > > Hi Chimera team, > I am new to the the Chimera and I found it is really nice and user friendly. > I have ChimeraX version 1.2.5 on Ubuntu 16.04 system. > I wanted to make movies using the animation tool in ChimeraX but my utilities tab only have two options Registration and updates. > How can I access the animation pane? > Best > Dilip Badgujar

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Re: [chimerax-users] [Chimera-users] .dae export for ChimeraX
by Tom Goddard 03 Dec '21

03 Dec '21

Hi Byrne, Thanks! So Blender can convert GLTF to Collada. The ChimeraX GLTF is binary and Collada is all text, so no surprise that the file size is much larger. If we add Collada support it would be produced directly from the ChimeraX scene, not converting from GLTF. But we have hundreds of new feature requests so I don't think Collada output is likely to be added soon, unless a funded project needs it. Tom > On Dec 3, 2021, at 9:48 AM, Byrne Pedit <bpedit(a)comcast.net> wrote: > > Hi Tom, > > A follow-up for future reference. Blender, the one recommendation I found on StackOverflow, is indeed capable of converting GLTF to DAE. But the conversion bloats the files by as much as 10x! In addition, the hierarchy is only partially preserved. I tried an on-line converter with even less satisfactory results. So I think this pathway is a bust. This might serve as a fair warning for ChimeraX developers to avoid an internal conversion from GLTF if introducing a DAE export option. > > > Byrne > > > > >> On Dec 2, 2021, at 2:22 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Byrne, >> >> I agree, OBJ and STL are very limited compared to Collada and GLTF. OBJ is supported by almost every 3D model program and STL is commonly used for 3D printing (single color) which is why they are in ChimeraX. GLTF is definitely the best option in ChimeraX for your case. >> >> There appear to be lots of programs that convert GLTF to Collada and the other direction too. But I have not tried any of them so don't have any recommendation. Let us know if you find one that works well -- other ChimeraX users may have the same need. >> >> A major stumbling block exporting 3D models from ChimeraX (or Chimera) is that they use vertex colors, while most of the non-biology 3D model world uses texture colors, and will simply ignore vertex colors losing all your color information. That example I linked to in the last email describes a relatively new ChimeraX feature to export texture colors (for limited cases, e.g. discrete colors only). >> >> Another common problem exporting molecular models for use in other software is that the file size and number of triangles is too large for the application that you want to use them in, often tens of millions of triangles or hundreds of Mbytes to Gbytes in size. The example also shows how to tell ChimeraX to limit the number of triangles. >> >> https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html <https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html> >> >> Tom >> >> Model from gltf export from linked ChimeraX example >> >> <spike.png> >> >> >>> On Dec 2, 2021, at 2:04 PM, Byrne Pedit <bpedit(a)comcast.net <mailto:bpedit@comcast.net>> wrote: >>> >>> Hello Tom, >>> >>> Thanks for the response. I tried the GLTF export, not recognizable by Xcode (the development platform for iOS and Mac OS). The only ChimeraX file options I’ve found to be openable are OBJ and STL. These are, however, problematic and unusable. >>> >>> But your hint of using GLTF as an intermediary offers an avenue for exploration, it’s not a format I’ve used. I see it supports scene graph hierarchy, absent with OBJ and STL( exported from ChimeraX anyway) so this is promising. Now to find a converter. >>> >>> The GLTF export link is informative, it may help further refine my approach. Interestingly, the molecule you’ve chosen for demo purposes appears to be the one, or a variant thereof, I’ve been testing with! >>> >>> Thanks again, >>> >>> Byrne >>> >>> >>>> On Dec 2, 2021, at 12:30 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>> >>>> Hi Byrne, >>>> >>>> We have long been interested in adding Collada format export of scenes from ChimeraX. Here is the feature request for that >>>> >>>> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485> >>>> >>>> But our scene export in ChimeraX has focused on GLTF format, as that has been the most requested. Here is an example showing GLTF export from ChimeraX (including texture colors). >>>> >>>> https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html <https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html> >>>> >>>> ChimeraX also exports OBJ, STL, X3D, VTK as shown in the save command docs >>>> >>>> https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats> >>>> >>>> Can you make use of GLTF files? If not, a quick solution might be to convert ChimeraX GLTF files to Collada with third-party software. >>>> >>>> Tom >>>> >>>>> On Dec 2, 2021, at 10:41 AM, Byrne Pedit via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >>>>> >>>>> ChimeraX is awesome and definitely superior to the original but for the inability to export as .dae (Collada). Is that possibly on the to-do list? This is important for those of us (just me?) writing interactive molecular apps for devices. It is the only satisfactory path I’ve found between a PDB file and SCNNodes/Scenes in iOS. (See the iOS app ‘BioMole’, free, if interested in an application.) >>>>> _______________________________________________ >>>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>>> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> >>>>> >>>> >>> >> >

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Re: [chimerax-users] [Chimera-users] .dae export for ChimeraX
by Tom Goddard 02 Dec '21

02 Dec '21

Hi Byrne, I agree, OBJ and STL are very limited compared to Collada and GLTF. OBJ is supported by almost every 3D model program and STL is commonly used for 3D printing (single color) which is why they are in ChimeraX. GLTF is definitely the best option in ChimeraX for your case. There appear to be lots of programs that convert GLTF to Collada and the other direction too. But I have not tried any of them so don't have any recommendation. Let us know if you find one that works well -- other ChimeraX users may have the same need. A major stumbling block exporting 3D models from ChimeraX (or Chimera) is that they use vertex colors, while most of the non-biology 3D model world uses texture colors, and will simply ignore vertex colors losing all your color information. That example I linked to in the last email describes a relatively new ChimeraX feature to export texture colors (for limited cases, e.g. discrete colors only). Another common problem exporting molecular models for use in other software is that the file size and number of triangles is too large for the application that you want to use them in, often tens of millions of triangles or hundreds of Mbytes to Gbytes in size. The example also shows how to tell ChimeraX to limit the number of triangles. https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html Tom Model from gltf export from linked ChimeraX example > On Dec 2, 2021, at 2:04 PM, Byrne Pedit <bpedit(a)comcast.net> wrote: > > Hello Tom, > > Thanks for the response. I tried the GLTF export, not recognizable by Xcode (the development platform for iOS and Mac OS). The only ChimeraX file options I’ve found to be openable are OBJ and STL. These are, however, problematic and unusable. > > But your hint of using GLTF as an intermediary offers an avenue for exploration, it’s not a format I’ve used. I see it supports scene graph hierarchy, absent with OBJ and STL( exported from ChimeraX anyway) so this is promising. Now to find a converter. > > The GLTF export link is informative, it may help further refine my approach. Interestingly, the molecule you’ve chosen for demo purposes appears to be the one, or a variant thereof, I’ve been testing with! > > Thanks again, > > Byrne > > >> On Dec 2, 2021, at 12:30 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Byrne, >> >> We have long been interested in adding Collada format export of scenes from ChimeraX. Here is the feature request for that >> >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485> >> >> But our scene export in ChimeraX has focused on GLTF format, as that has been the most requested. Here is an example showing GLTF export from ChimeraX (including texture colors). >> >> https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html <https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html> >> >> ChimeraX also exports OBJ, STL, X3D, VTK as shown in the save command docs >> >> https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats> >> >> Can you make use of GLTF files? If not, a quick solution might be to convert ChimeraX GLTF files to Collada with third-party software. >> >> Tom >> >>> On Dec 2, 2021, at 10:41 AM, Byrne Pedit via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >>> >>> ChimeraX is awesome and definitely superior to the original but for the inability to export as .dae (Collada). Is that possibly on the to-do list? This is important for those of us (just me?) writing interactive molecular apps for devices. It is the only satisfactory path I’ve found between a PDB file and SCNNodes/Scenes in iOS. (See the iOS app ‘BioMole’, free, if interested in an application.) >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> >>> >> >

1 0

Re: [chimerax-users] [Chimera-users] .dae export for ChimeraX
by Tom Goddard 02 Dec '21

02 Dec '21

Hi Byrne, We have long been interested in adding Collada format export of scenes from ChimeraX. Here is the feature request for that https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485> But our scene export in ChimeraX has focused on GLTF format, as that has been the most requested. Here is an example showing GLTF export from ChimeraX (including texture colors). https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html ChimeraX also exports OBJ, STL, X3D, VTK as shown in the save command docs https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats Can you make use of GLTF files? If not, a quick solution might be to convert ChimeraX GLTF files to Collada with third-party software. Tom > On Dec 2, 2021, at 10:41 AM, Byrne Pedit via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > ChimeraX is awesome and definitely superior to the original but for the inability to export as .dae (Collada). Is that possibly on the to-do list? This is important for those of us (just me?) writing interactive molecular apps for devices. It is the only satisfactory path I’ve found between a PDB file and SCNNodes/Scenes in iOS. (See the iOS app ‘BioMole’, free, if interested in an application.) > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users >

1 0

coloring clipped surface only separately
by Y. Mutum 02 Dec '21

02 Dec '21

Hi Elaine and Team My question relates on how we can color the 'clipped surface only' using a different color independently. This is without messing up the color of the outer surface of the model. Suppose the outer surface of the pdb-model has been colored by hydrophobicity (mlp). Then, I slice the model using the 'side view' tool. Now, using the 'surface cap' command, I can get a clipping plane which is colored 'bychain'. However, if I try to color the clipped surface using a different color, the entire hydrophobicity surface is no longer there. These are my commands below. Is there a way to color the clipped surface by a different color? If not is there a way around? The commands I have used are: >>> open 6g2j; hide all; >>> color #1 green; color /B-G,I,Q,P,R,W,q yellow; Then using the side view tool, clip the surface of the model to get a slice. I am trying to clip in the plane containing Chain D and B. >>> mlp #1; >>> surface cap true; Then, I can get a clipping plane colored by-chain. If I then type >>>color zone #1 near #1 distance 5 Then, I can get the clipped surface to change its color but this messes up the hydrophobicity of the outer surface. Thus, 1. Is there a way to color the clipped surface separately, while not messing up with the outer surface coloring (hydrophobity in this case)? 2. Suppose I want to remember this clipping plane for another ChimeraX session and would like to avoid the manual clipping using the 'Side view'. Using command line, is there a way to get back to the clipping plane? Similar to 'camera matrix' command, but, with the 'sectioned plane' also included. Thanks Yaikhomba

2 2

measuring rotation between two homologous PDB models
by Y. Mutum 28 Nov '21

28 Nov '21

Hi Elaine and ChimeraX Team My query relates to measuring rotation between two subunits from homologous models in ChimeraX. Here, I have first aligned the two models on one of sub-domains of these multi-domain complex. Then, without moving the models, the plan is to calculate the rotation in another domain, between the 2 models, apart from measuring the translational shift. So, * Align Chain /L,M (model #1, PDB:6g2j ) and Chains /5,4 (model #2, PDB:6rfr). * Calculate rotation of Chain /F (model #1, PDB:6g2j) and Chain /B (model #2, PDB:6rfr). I am using the following commands: -- open 6g2j; open 6rfr; -- match #1/L,N to #2/5,4 pair ss; -- measure rotation #1/F toModel #2/B coordinateSystem #1/F showAxis true showSlabs true; The log report is: Position of 6g2j #1 relative to 6rfr #2 in 6g2j #1 coordinate system: Matrix rotation and translation 0.80441124 0.40360431 -0.43591986 67.76279700 0.18783349 0.52334489 0.83116106 -121.82969657 0.56359661 -0.75047565 0.34517410 202.31442783 Axis -0.83978100 -0.53070022 -0.11456502 Axis point 0.00000000 87.13355460 206.39866592 Rotation angle (degrees) 70.33834463 Shift along axis -15.42901832 Thus, ChimeraX is calculating a rotation of ¬70 degrees, which is clearly the case. The visual inspection suggests, that the rotation should be no more than ~15-20 degrees. I am not sure where I am going wrong. Could you please help? Thanks Yaikhomba

3 5

Exporting Measure and Color Blob data
by BINGHAM Dominic 25 Nov '21

25 Nov '21

Hello, I am wanting to get the volumetric data of several blobs in a manner I can easily export and analyse. I am using the Measure and Color Blobs tool and I can see the data I need. However, I have lots of models, with lots of blobs. That means me stopping and writing down the volume data each time I click is not very efficient. So is there anyway I can export all the volume data per each selected blobs per each image into one file? Thanks, Dominic Bingham

2 1

Match the scale of OBJ and volume
by Roden Deng Luo 24 Nov '21

24 Nov '21

Hi, As shown in the screenshot, I have opened one volume and one obj. But they should have the same scale. How can I achieve this? Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 2

Color volume series by per voxel variance?
by Oliver Clarke 24 Nov '21

24 Nov '21

Hi all, Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame? When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume. Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible? Cheers Oli

3 7

ChimeraX import multiple positions of the same .pdb structure
by Frey, Lukas 23 Nov '21

23 Nov '21

Dear Elaine, I have an external file with a transformation matrix (orientation and translation) for a .pdb structure and I would like to apply the transformation in ChimeraX to a .pdb file. I’m aware that ChimeraX needs a matrix like [[1,1,1],[2,2,2],[3,3,3],[x,y,z]], where the first 3 columns are the orientation the last column the x,y,z translation positions. One can load a new orientation/translation into chimeraX with the „open“ command: https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html in the command line of chimeraX I had to type in: open path-to-file/test.positions models #1 childModels true matchNames true my test.positions file is a .txt file containing the name of the .pdb structure and transformation matrix and I already loaded the .pdb structure before I applied the transformation matrix. Below you can find the input of the transformation matrix file, called text.positions: 6y2l.pdb,-0.6515591636522021,-0.6041757901381976,-0.45873987277293393,0.09148867345316551,-0.662890582358989,0.7431055769199559,-0.7530607405054541,0.44220774578318395,0.48718767500700594,30.0,20.0,30.0 If I apply the open command in chimera somehow it leads to a distortion of the .pdb protein structure. If I check the transformation position of the model with „view matrix“, then I have the following output: view matrix camera position: 0.94464,-0.25925,-0.20113,-578.87,-0.29451,-0.94014,-0.17144,1242.4,-0.14464,0.22118,-0.96445,-8143.8 model positions: #1,-0.65156,-0.60418,-0.45874,0.091489,-0.66289,0.74311,-0.75306,0.44221,0.48719,30,20,30,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0 Somehow the transformation matrix is only applied to #1 but not to #1.1 and #1.2, do you have an idea what I have to change? If I save the transformation matrix of the distorted .pdb structure via the save command: save path-to-file/test_2.positions models #1 childModels true I have the following output: 6y2l.pdb,-0.651559163652,-0.604175790138,-0.458739872773,0.0914886734532,-0.662890582359,0.74310557692,-0.753060740505,0.442207745783,0.487187675007,30,20,30 metal coordination bonds,1,0,0,0,0,1,0,0,0,0,1,0 missing structure,1,0,0,0,0,1,0,0,0,0,1,0 The goal in the future is to load several positions (1 … 100) of the same .pdb structures. Best, Lukas Lukas Frey Visiting Postdoctoral Associate UMASS Medical School Worcester Grigorieff Laboratory

3 2

Re: [chimerax-users] meshmol in chimeraX
by Tom Goddard 23 Nov '21

23 Nov '21

Hi Vijay, The meshmol command from Chimera which converts a surface mesh from wire edges to cylinder edges (making a fake molecule) is not yet in ChimeraX. But I can add it pretty easily, maybe tomorrow if time permits. Tom Icosahedral cage shown with wires and with meshmol cylinders > On Nov 18, 2021, at 2:38 PM, Vijay Reddy <reddyv(a)scripps.edu> wrote: > > Hi Tom, > > Greetings! Hope are staying safe and healthy. > > I am finally transitioning to chimeraX. > > Could you please tell me what is the equivalent of > > the chimera command “meshmol #26 6” in chimeraX > > Many thanks, > Vijay >

2 3

Toolshed
by Moustafa, Ibrahim M. 23 Nov '21

23 Nov '21

Dear ChimeraX, Trying to install iSolde but toolshed page seems to be down! Is there another link to https://cxtoolshed.rbvi.ucsf.edu ? ChimeraX Toolshed<https://cxtoolshed.rbvi.ucsf.edu/> Resource for Biocomputing, Visualization amd Informatics (RBVI), and its precursor, the Computer Graphics Laboratory (CGL), develops cutting-edge interactive software tools and advanced web-based computational resources that provide integrated visualizations and analyses of molecular structures and related non-structural biological information. cxtoolshed.rbvi.ucsf.edu Thanks, Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park State College, PA16802 Phone: (814) 863 5940 Fax: (814) 865 7927

2 2

Question about Chimerax
by JANE LEE 22 Nov '21

22 Nov '21

Hi, I was wondering how/if I could open saved session files from Chimera in Chimerax? Also, when I tried to open a protein in Chimera, it opened. But when I tried to open the same protein in Chimerax, it only showed up as atoms and I received the message "start residue of secondary structure not found." I was wondering if you have any suggestions for troubleshooting? Thank you! Regards, Jane

2 1

ChimeraX AlphaFold2
by Ichcharisma 20 Nov '21

20 Nov '21

Hi ChimeraX Dev I wondering if I can run oligomer prediction on ChimeraX AlphaFold features. As we can do it with others colabfold version out there. Thank you

4 6

Feature request: windowsize to be stored with session
by mailman-bounces＠cgl.ucsf.edu 18 Nov '21

18 Nov '21

From: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> Date: November 18, 2021 at 8:47:33 AM PST Dear all, I would like to suggest that the current windowsize is associated with a ChimeraX session. This is particularly useful when making figures in a reproducible manner (if I am not mistaken, when opening a .cxs file it will open it with the same windowsize that has been used for the last chimera session, rather than the one that was used when the session was created). I am aware that the windowsize can be specified in a script file. Thanks a lot for your consideration : ) Best, Matthias

3 2

Re: [chimerax-users] [Chimera-users] chimera, H-bonds
by Elaine Meng 18 Nov '21

18 Nov '21

> On Nov 18, 2021, at 11:37 AM, Rio Aquarius via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Developer, > I have a specific task for ChimeraX. I want to show H-bonds and hide all amino acid residues. But when I hide amino acid residues, all H-bonds I need disappear. Is there a way to do what I want? Dear Rio, The H-bond displays are lines (pseudobonds) drawn between atoms. When you hide those atoms, the H-bonds are also hidden. I don't understand why you would want to display a bunch of lines in space without any atoms, as you won't be able to see most of the valuable information from the calculation. However, I will explain how to do it: In ChimeraX, there is no pseudobond option to display even when its atoms are hidden. The only way to make it look like the H-bond lines are shown when you can't see the atoms (and/or ribbons) is to make the atoms (and/or ribbons) 100% transparent with the "transparency" command. Example commands: open 2gbp hbonds reveal true transparency 100 target ar <https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

getting sequences into the Structure Prediction
by Marc Pusey 17 Nov '21

17 Nov '21

Hi - I may be missing something very obvious, but... I am trying to input and use protein sequences for structure predictions using the AlphaFold feature of ChimeraX. I've not had any problems when the sequence can be obtained from a UniProt file, but several of the proteins I'm working with do not have such a file available. Additionally, there is going to come a time where I will want to see what the consequences are from making mutations to those sequences that are available from UniProt. The input gives the option of either Paste or UniProt, but I've not found a way to do a simple cut and paste to put in the sequence. I'm using a Mac running Mojave, version 10.14.6. Thanks! Marc Pusey -- Marc Pusey

3 5

Viewing all frames of trajectory at once
by German Barcenas 17 Nov '21

17 Nov '21

Hello, I've made a trajectory of some similar frames that are stored as an .xtc file. I can upload this with my defined topology file (.pdb) and see each frame individually. Currently I can create a picture of each frame with the frame centered on some residue (SQA) with: perframe "save ~\snapshot_$1.png" frames 10;coordset #1 holdSteady /A:SQA This creates individual pictures for each frame which is nice. I was wondering how one makes a picture with all 10 frames superimposed on each other. I'd also like to change all but the 1st frame to be transparent. I'm aware of the transparent command, which I presume I'd apply to all frames except the 1st, but I'm not sure how to display all frames at once. I'm also struggling on the 1st frame only condition. This is my current attempt: perframe "transparency 0 ALL" frames 1;perframe "transparency 25 ALL" frames 9;coordset #1 holdSteady /A:SQA Thanks, -- German Barcenas Ph.D Candidate | Materials Science and Engineering Materials Modeling and Theory Group Boise State University

2 2

Model info editing
by Eric Pettersen 16 Nov '21

16 Nov '21

Hi all, The current daily build (not 1.3 release candidate) has a new feature that may be of general interest. You can change the name/ID of a model in the Model Panel by double clicking on the corresponding field and entering a new value. --Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

Feature request regarding clipping planes
by Pranav Shah 15 Nov '21

15 Nov '21

Hi Team, Chimera has really nice clipping planes visibility and UX in comparison to ChimeraX. While it may take some effort to include the middle-click based riflling through planes shortcut, in the short term would it be possible to change the color of the clipping planes to a color that isnt gray? Currently, it is quite hard to see the clipping planes in the default view (see attached image). Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

4 8

Re: [chimerax-users] Any interest in reading ModelArchive metadata from mmCIF files?
by Tom Goddard 12 Nov '21

12 Nov '21

Hi Elaine, This is related but a little different from what Ben was asking. It is different because the template and scoring data in the mmCIF tables could be shown no matter how the mmCIF file is loaded -- it would not be limited to fetching from ModBase. Maybe Ben has an opinion about how desirable it is to put the Chimera ModBase fetch capability into ChimeraX, and whether it is more or less desirable than making the new mmCIF tables accessible in ChimeraX, to help figure out priorities. Tom > On Nov 12, 2021, at 3:05 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Chimera had a ModBase Fetch: > > "a SwissProt, TrEMBL, GenPept or PIR accession code will be used to fetch comparative models in PDB format from ModBase (associated information will be shown in a model list)" > > https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modbase.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modbase.html> > > ...where "model list" is the same dialog as used to show Modeller results. Now that ChimeraX has a Modeller Results dialog for displaying the output from Comparative Modeling and Model Loops, could consider adding analogous Modbase fetch capability. > > I can make a ticket if anybody thinks that's a good idea. > > Elaine > > >> Begin forwarded message: >> >> From: Tom Goddard via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> >> Subject: Re: [chimerax-users] Any interest in reading ModelArchive metadata from mmCIF files? >> Date: November 12, 2021 at 2:56:49 PM PST >> To: Ben Webb <ben(a)salilab.org <mailto:ben@salilab.org>> >> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> >> Reply-To: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> >> >> So it looks like only ModBase would currently benefit from ChimeraX reading template sequences and alignments. I do not think it would be too hard to implement it. I've made a ChimeraX feature request for that >> >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5601 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5601>

2 1

Any interest in reading ModelArchive metadata from mmCIF files?
by Ben Webb 12 Nov '21

12 Nov '21

Do you have any plans to extend ChimeraX's mmCIF reader to parse and display metadata on theoretical models, such as quality scores or the alignments to template structures? The folks at PDB have recently done a lot of work to standardize this metadata in the MA mmCIF dictionary: https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/ The dictionary has already been adopted by ModelArchive (e.g. AlphaFold2 models) and by ModBase (Modeller models) and I believe that other repositories such as SwissModel are also moving in that direction. See e.g. mmCIF downloads at https://www.modelarchive.org/doi/10.5452/ma-bak-cepc-0250 https://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?databaseID=Q1… (My ulterior motive: we've previously built Chimera web data files to download a ModBase model and the accompanying alignment, and display them in Chimera; now that this data is embedded in the mmCIF file, in principle ChimeraX could do this itself in a less clunky and not ModBase-specific fashion.) Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

2 1

Fit in map sequentially with global search?
by Oliver Clarke 12 Nov '21

12 Nov '21

Hi, I frequently use the "global search" option of fitmap in chimera to identify the orientation of proteins or fragments in my map. Fitmap has an option, "sequence", allowing the sequential fitting of multiple structures to a map, after subtracting the density corresponding to the previous fit, but this is not compatible with global search. Would it be possible to add an option to fitmap in ChimeraX such that it considers clashes with designated existing models? This would be useful when one is trying to fit the density of a weakly occupied binding partner in the context of a larger known structure. Presently, when one uses fitmap with global search in such a case, the binding partner frequently gets sucked in to the stronger density for the host protein, even when the density for the binding partner is visually clear. Cheers Oli

3 3

chimera x : how to increase font size of the command line display?
by Rangarajan, Amith 12 Nov '21

12 Nov '21

Dear All, I am wondering if there is a way to increase the font size of the command line display? I found this post with tom's comment https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016776.html [Chimera-users] Make command-line text bigger<https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016776.html> Hi Lothar, I don't know what problem you are encountering using ReadStdin on Windows. It may have something to do with Windows not allowing stdin/stdout for GUI apps. www.cgl.ucsf.edu not sure if things have changed after that. thanks , amith

2 1

saving PDB
by Noriega, Heather 11 Nov '21

11 Nov '21

Hello, I am going to attach my command line. OK, so I created a specific capsid that is not all one monomer. It has 3 different monomers in a specific ratio. I have toggled around with different options below to try to save in PDB, the save option from my understanding should be the selected only because this capsid was created using the matchmaker. I tried display only as well just to try to see if that worked. I also have used the relative model from biological assembly of 1LP3 and tried to save or not save options and have kept all consistent with hybrid 36 (default). All these options say "saved", however when i go to open any of them, they do not at all. My objective is to save the whole capsid so when I open it I can perform the density map to measure the volume inside. The weird part of this is when I open these saved creations in Chimera they will open how I want them to, but not in ChimeraX. I am not too sure why. Please help me and I hope everyone is well, have a good night. UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open.pdb" models #2-61 displayedOnly true relModel #1 close session open "C:\Users\Haten\Documents\AAVgene\why wont you open.pdb" format pdb UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open 2.pdb" models #2-61 selectedOnly true close session open "C:\Users\Haten\Documents\AAVgene\why wont you open 2.pdb" format pdb Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

3 7

An inquiry
by Victor Ejigah 11 Nov '21

11 Nov '21

Hi Elaine, I am using chimeraX for protein analysis and simulations and recently, we have a question we want to explore by first simulating before going to the wet lab. We want to conjugate a polymer of different molecular weight to an antibody and thereafter determine the impact of the MW of each polymer on the binding affinity of the mAB to its ligand. Therefore, we want to know 1) Can we create polymers of different sizes with chimera? If not, can you recommend alternatives? 2) What tool can we use for conjugation( assuming chimera can be of help)? 3) Can such conjugates be exported to Chimera1.5 for MD ensemble since Chimera X does not have this feature? I will be most glad to hear from you soon. Kind regards, Victor (PhD student @Howard University)

2 3

vop min/max threshold
by Stapleton kevin2017/4/3 10 Nov '21

10 Nov '21

Hello everyone! just trying to get my head around a small problem, but one my brain turns into spaghetti. I am trying to save a density from molmap with a threshold range of given values. for example: open 2gbp molmap #1 10 >From the resulting density (now ID #2) I want to save the map at a very narrow threshold range. for example the current range is 0.0-0.528. But I would like to save the map with a "restricted" level of 0.26-0.27. I have been playing with the vop min/max threshold xxx set 0/1 commands but I keep getting turned around. here is what I did: open 2gbp molmap #1 10 - produces a new map ID #2 vop threshold #2 minimum 0.26 set 0 vop threshold #3 maximum 0.27 set 1 I used the set 0/1 because I want the range 0.26-0.27 to have the density values and anything outside of that to have zero. Like a mask in relion. But for my specific case relion_mask wont work as well. Somewhere I am turning the options around and it has my brain flattened. Any help is appreciated. All the best and thanks for making my science life 1Million times easier with your wonderful program :-) Kako

2 3

Improved VR support in ChimeraX
by tolung.bio＠gmail.com 09 Nov '21

09 Nov '21

Hi, The VR support in ChimeraX and meeting functionality has a great potential especially for teaching and educational purposes. Are you planning to improve that to bring it to the same level as Nanome (or close)? For example, a dedicated VR GUI interface for better VR usability? Cheers, Gökhan

2 1

Labelling w.r.t Secondary structure elements
by Gupta, Arun 09 Nov '21

09 Nov '21

Hello, I was wondering is there a quick fix way around by which we can define in an automated fashion the numbering and further labelling of secondary structural elements labels, alongside the structure, based on “dssp” described symbol notation "for example starting from α1/β1-α10/β14 " for any protein instead of manually labelling later in Power point. Thanks a lot! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

3 7

Removing and Testing Bundles
by Zeng, Jingrou 09 Nov '21

09 Nov '21

Hello, I am working on a selector bundle and need to actively reload it into ChimeraX every time I make changes to the code. I have followed the instructions on the tutorials and successfully loaded my bundle into ChimeraX using 'devel install [path]'. I then tried to reload the bundle after I have made changes to the code with commands 'devel clean [path]' followed by 'devel install [path]'. But ChimeraX didn't receive my update to the bundle. I tried reinstalling ChimeraX, the selector bundle still works without a separate installation and it doesn't register any updates I have made. I am using macOS and have experimented with both daily build and 1.2.5. Is there a way of completely removing the old version of my bundle? What is the best way to do bundle reloading and testing in ChimeraX? I also want to use the print command for debugging, but printing doesn't seem to work with the ChimeraX log, is there a separate log for this situation? Thank you for your help. Regards, Katie

2 1

Re: [chimerax-users] Measuring volume inside virus capsid
by Tom Goddard 05 Nov '21

05 Nov '21

Hi Heather, Your "No symmetry for #1" error when you use command "sym #2 symmetry #1 copies true" is likely because you opened the 1LP3 (#1) PDB file in mmCIF format instead of using the command I suggested "open 1lp3 format pdb" which opens it in PDB format. The ChimeraX sym command currently only uses the "biological assembly" information from PDB format, not mmCIF format as described in the sym command documentation https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry> In the future please copy and paste commands and the error message into your email. That gives us enough info to help you and is better than a screenshot. Tom > On Nov 5, 2021, at 6:46 PM, Noriega, Heather <heather.noriega(a)bison.howard.edu> wrote: > > Hi, > > Yes, so I have read your manual about the symmetry and have been trying to do what you suggested, before you suggested it (the symmetry portion). That is why I reverted to the one-by-one. It keeps giving me this error. I have also tried using the chain /A for the symmetry and it does create the complete icosahedral, but once I try to complete the molmap it only does the single monomer. I don't know what to do. > > Thank you, > > Heather Noriega > PhD-Pharmaceutical Science student > Howard University > heather.noriega(a)bison.howard.edu <mailto:heather.noriega@bison.howard.edu> > 520-203-1883 > > > On Fri, Nov 5, 2021 at 6:26 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Heather, > > I looked at the ChimeraX session and see you opened 60 copies of your alphafold model, then ran matchmaker 60 times to align those to the 1LP3 virus capsid, then ran molmap 60 times. That is a lot of tedious work and does not get quite what you want. So here are some commands to try go get the enclosed volume. > > open 1lp3 format pdb > open ~/Downloads/ChimeraX/AlphaFold/prediction_23/best_model.pdb > matchmaker #2 to #1 > sym #2 symmetry #1 copies true > molmap #3 12 > volume #4 level 0.07 > # Choose "blob" mouse mode under the "Right Mouse" toolbar tab and right click (option key on Mac) the volume surface to color it. > surface splitbycolor #4.1 > view position #5 sameAs #4 > hide #4,5.1 model > measure volume #5.2 > -> 2.5 million cubic Angstroms > > Here I aligned a single copy of the AlphaFold model (#2) to the 1lp3 capsid monomer (#1) with matchmaker, then applied the symmetry of 1lp3 to the AlphaFold model to produce all 60 copies (#3), then made a density map from those 60 copies (#4), then set a low enough density map threshold so that their are no holes connecting the inside and outside of the capid, then colored the outside surface different from the inside with the blobs mouse mode, then split that two color surface into two pieces (outside #5.1, inside #5.2), then realigned the split surface to the density map (it was a bug that it did not preserve the alignment), then measured the volume of the inside surface. > > If you have questions about any of these commands the ChimeraX user manual has thorough documentation on all of them, so read about them. > > I described a slightly simpler case of finding the interior volume of 1lp3 on the ChimeraX Recipes web page. > > https://rbvi.github.io/chimerax-recipes/virus_volume/virusvol.html <https://rbvi.github.io/chimerax-recipes/virus_volume/virusvol.html> > > Tom > > >> Begin forwarded message: >> >> From: "Noriega, Heather" >> Subject: measuring volume >> Date: November 5, 2021 at 2:25:42 PM PDT >> To: Tom Goddard >> >> Hello Tom, >> >> I hope this email finds you well. I am very grateful for your email a couple days ago with chimeraX and trying to compute the interior volume in a virus capsid shell. I am very new to all this molecular modeling software, but am trying very hard to learn and understand. I have been working on a few different capsids particularly through alpha fold predictions on ChimeraX. I have created this one below through one-by-one aligning the predictions to create T=1 (1LP3 as biological assembly reference). Now, I one-by-one again used the molmap application for each copy and changed to volume level 0.676 and colored dark blue. My issue is when I go to measure volume it says the surface selected is wrong. I am unsure how to fix it or if I can fix it. Also, I do not know if this has anything to do with it, but I am using a Windows computer, I have noticed most of your videos are done through apple. Would this make a huge difference? I await your response and again thank you very much for your help. >> >> Thank you, >> >> Heather Noriega > > > > >> On Nov 3, 2021, at 11:49 AM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Heather, >> >> Here is a tricky way to compute the interior volume in a virus capsid shell in ChimeraX. >> >> open 1LP3 >> sym #1 assembly 1 copies true >> molmap #2 12 >> volume #3 level 0.676 >> # Choose "blob" mouse mode under the "Right Mouse" toolbar tab and right click (option key on Mac) the volume surface to color it. >> surface splitbycolor #3.1 >> hide #4.1 model >> measure volume #4.2 >> -> 2.6 million cubic Angstroms. >> >> The idea is to make a low resolution (12 Angstrom) density map from the atomic model, low resolution so there are not holes in the capsid, set the map threshold so there are no holes connecting the inside and outside, then color the outside layer with the "pick blob" mouse mode, then split the surface by color (producing inside and outside surfaces), then measure the volume enclosed by the inside surface. >> >> Tom >> >> Here's a cut in half view showing the interior surface produced by the above example >> >> >>> On Nov 3, 2021, at 11:21 AM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> I don't know if it would work on your specific case, but there is a "3V" server that makes maps that fill cavities and tunnels that you could try. Namely, I don't know if it works for fully enclosed cavities. >>> >>> <http://3vee.molmovdb.org/ <http://3vee.molmovdb.org/>> >>> >>> If it gave a suitable output (a map blob that fits inside your capsid) then you can use "measure volume" after opening it in ChimeraX and showing its isosurface. >>> >>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume>> >>> >>> I'm sure there are other creative ways if you think about it... like trying to make a sphere that fits inside and calculating the volume of the sphere from the standard geometric formula. >>> >>> I was trying to think of a way involving a low-resolution surface (e.g. from using "molmap" on the capsid atoms) and "volume onesmask" but couldn't come up with anything. The problem with just using a molecular surface or low-res surface from molmap is that it is hollow, and the volume calculation will just include the shell with the atoms, not the big empty part inside. >>> >>> As you can see, none of these are like a one-step thing that is already figured out for you. Part of being a PhD student is trying to solve problems that haven't been worked out for your specific situation! >>> >>> Elaine >>> >>>> On Nov 3, 2021, at 10:38 AM, Noriega, Heather via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> >>>> What other ways can you measure the inter space of the icosahedral? >>>> >>>> Thank you, >>>> >>>> Heather Noriega >>>> PhD-Pharmaceutical Science student >>>> College of Pharmacy >>>> Howard University >>>> heather.noriega(a)bison.howard.edu <mailto:heather.noriega@bison.howard.edu> >>>> 520-203-1883 >>>> >>>> On Wed, Nov 3, 2021, 12:09 PM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >>>> Hi Heather, >>>> I guess my first question is "why would you want to do that?" If the goal is to measure the cavity volume, there may be other ways. I'm not aware of any ChimeraX capability to fill it with waters (you may have to write your own code if that's what you really want to do). >>>> >>>> In general you can count the waters (or any other residue type) in some structure using a similar method to what I described recently on the chimera-users list, except that to show the Selection Inspector you click the green magnifying glass on the top bar icons of ChimeraX instead of the lower-right corner of the Chimera window. >>>> <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-November/018182.html <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-November/018182.html>> >>>> >>>> I hope this helps, >>>> ELaine >>>> ----- >>>> Elaine C. Meng, Ph.D. >>>> UCSF Chimera(X) team >>>> Department of Pharmaceutical Chemistry >>>> University of California, San Francisco >>>> >>>>> On Nov 3, 2021, at 6:20 AM, Noriega, Heather via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> >>>>> Good morning, >>>>> I am working on trying to find a measurement inside my alphafold prediction icosahedral. My advisor mentioned using the water molecules to fill the inside and then use a counter of some sort. I have no idea how to start this, I have been reading the volume commands but am still having a hard time. Can you direct me to 1) fill only the inside of my icosahedral? and 2) how to count the water molecules inside? >>>>> Thank you, >>>> >>>> _______________________________________________ >>>> ChimeraX-users mailing list >>>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>>> Manage subscription: >>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >>> >> >

1 0

A couple questions
by Noriega, Heather 05 Nov '21

05 Nov '21

Good morning, I am working on trying to find a measurement inside my alphafold prediction icosahedral. My advisor mentioned using the water molecules to fill the inside and then use a counter of some sort. I have no idea how to start this, I have been reading the volume commands but am still having a hard time. Can you direct me to 1) fill only the inside of my icosahedral? and 2) how to count the water molecules inside? Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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alpha-fold error
by Moustafa, Ibrahim M. 05 Nov '21

05 Nov '21

Dear all, I am trying to use alpha fold in ChimeraX but I get the following error during computing multiple sequence alignmenet step: -------------------------------------------------------- TypeError ________________________________ 2 frames ________________________________ <ipython-input-1-a242dc837c9a><https://localhost:8080/#> in multiple_seq_align(dbs) 247 for i, result in enumerate(db_results): 248 from alphafold.data import parsers --> 249 msa, deletion_matrix, target_names = parsers.parse_stockholm(result['sto']) 250 e_values_dict = parsers.parse_e_values_from_tblout(result['tbl']) 251 e_values = [e_values_dict[t.split('/')[0]] for t in target_names] TypeError: cannot unpack non-iterable Msa object --------------------------------------------------------- I followed the instructions of ChimeraX tutorial. I was able to use it successfully before, but not sure why I keep getting this error. Any idea what could be wrong? I use ChimeraX version 1.3 (09-08-2021) Thanks for help Ibrahim

2 2

Residue priority for Matchmaker alignment?
by Steven Truong 04 Nov '21

04 Nov '21

Dear ChimeraX Admins, I have a question about the Matchmaker (mmaker) command. If I wanted to specify which residues to prioritize in the alignment, how would I specify that in the command line? Is there a way to do this without changing the alignment algorithm/scoring matrix? I have tried tinkering with the matrix but wasn’t able to get it to work. I see that you can specify which chains to align, but I can’t seem to find the equivalent for residue ID numbers. Thank you for your help, Steven Truong Vendruscolo Lab Cambridge University [cid:280F6707-7208-4DBD-9A6C-ED9A0DF8E3BF]

2 1

How to open .py file downloaded from MOLEonline in ChimeraX?
by Kate Kim 01 Nov '21

01 Nov '21

Hello, I've been using Chimera in the past for opening downloaded .py files from MOLEonline to visualize tunnels in my structure. When I try to do the same in ChimeraX, I get the following error: Traceback (most recent call last): File "/Users/katekim/Downloads/mole_channels_6Qzq10eGEqLciv3DpeS8Q_1_chimera.py", line 1, in <module> import chimera, _surface, numpy ModuleNotFoundError: No module named 'chimera' Error opening python file /Users/katekim/Downloads/mole_channels_6Qzq10eGEqLciv3DpeS8Q_1_chimera.py toolshed show Any suggestions on the best approach to visualize MOLE channels using ChimeraX? Thank you, Kate

3 3

Making multiple icosahedral pentamers (assembly 3)
by Noriega, Heather 01 Nov '21

01 Nov '21

Hello, I am trying to make different monomer amounts of the icosahedral for my alphafold prediction. Now, I am able to use 1LP3 as my reference to create a icoshedral pentamer, but that is only 5. I would like to be able to do 10-mer, 15-mer, 20-mer, etc. I however can not seem to connect the pentamers to create the portions of virus capsid. Can you direct me? Thank you, Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega(a)bison.howard.edu <mailto:heather.noriega@bison.howard.edu> 520-203-1883

2 2

mmcif assemblies for alphafold prediction
by Noriega, Heather 30 Oct '21

30 Oct '21

Hello, I am trying to create an asymmetrical assembly similar to 4 and 6 with an alphafold prediction. There are no mmCIF assemblies connected with this prediction, is there a way to add the assemblies, if so how? Or is there another way to create this figure without the assembly? Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

2 4

Distances in the 3D map - visualisation analysis
by Dmitry Semchonok 29 Oct '21

29 Oct '21

Dear colleagues, I would like to measure the distances of within my 3D map - so I want to draw the arrows from the center of the map to the periphery in different directions and probably depth. (I want to have arrows and an length) Do you have any tips how to do that? Thank you Sincerely, Dmitry

2 1

Unit cell box
by Diego Sebastian Ferrero 27 Oct '21

27 Oct '21

Dear all, I am trying to make a figure using ChimeraX to show the contents of the unit cell in one protein structure. I would like to show the cell box with the asymmetric unit (similar to that box obtained in chimera using “Tools>Higher Order Structure>Crystal Contacts” ) but ChimeraX apparently doesn’t recognize the command returning the following message in the log window: unitcell outline Unknown command: unitcell What I’m doing wrong? Is it the right command to show the box? Thanks in advance, Diego

2 2

ChimeraX bug report submission
by Samuel Haysom 27 Oct '21

27 Oct '21

i want to show just the CA atoms of a selection of residues (starting with the rest of the model shown as a cartoon). To do this I am trying to use a command like this: show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799@CA target a But this doesn't do anything. If I take off the @CA bit I can show all the atoms in the residue. Full .cxc is as follows: open 5ljo open 5d0o hide #1,2 atoms show #1,2/A cartoons color #1,2/A rgb(0.252,0.680,1.000) color #1,2/B rgb(0.000,0.831,0.321) color #1,2/C rgb(1.000,0.861,0.137) color #1,2/D rgb(1.000,0.400,0.100) color #1,2/E rgb(0.780,0.000,0.400) ### Align barrels ### # mmaker #2/A:435-810 to #1/A:435-810 view matrix model #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.82647,-0.51941,0.21716,224.85,-0.53861,0.61724,-0.57351,177.83,0.16385,-0.59096,-0.78989,191.81,#2.1,1,0,0,0,0,1,0,0,0,0,1,0 ### Color EPR regions ### color #1,2/A:424-447 green color #1,2/A:454-518 red color #1,2/A:348-423 dark orange ### Create Morph ### morph #1,2 frames 40 ### Show single mutant CA ### ### New positions ### show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799@CA target a color #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799 magenta ### Existing Positions ### show #3/A:435,499,501,535,564,751,793 target a color#3/A:435,499,501,535,564,751,793 purple Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.3.dev202110261153 (2021-10-26) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 5ljo Summary of feedback from opening 5ljo fetched from pdb --- warnings | Atom H is not in the residue template for LEU /B:22 Atom H is not in the residue template for CYS /C:25 Atom H is not in the residue template for GLU /D:26 Atom H is not in the residue template for GLU /E:24 Atom H is not in the residue template for PHE /A:24 5ljo title: E. coli BAM complex (BamABCDE) by cryoEM [more info...] Chain information for 5ljo #1 --- Chain | Description | UniProt A | Outer membrane protein assembly factor BamA | BAMA_ECO45 B | Outer membrane protein assembly factor BamB | BAMB_ECOLI C | Outer membrane protein assembly factor BamC | BAMC_ECOLI D | Outer membrane protein assembly factor BamD | BAMD_ECO57 E | Outer membrane protein assembly factor BamE | BAME_ECOL6 > open 5d0o 5d0o title: BamABCDE complex, outer membrane β barrel assembly machinery entire complex [more info...] Chain information for 5d0o #2 --- Chain | Description | UniProt A | Outer membrane protein assembly factor BamA | BAMA_ECOLI B | Outer membrane protein assembly factor BamB | BAMB_ECOLI C | Outer membrane protein assembly factor BamC | BAMC_ECOLI D | Outer membrane protein assembly factor BamD | BAMD_ECOLI E | Outer membrane protein assembly factor BamE | BAME_ECOLI > hide #1,2 atoms > show #1,2/A cartoons > color #1,2/A rgb(0.252,0.680,1.000) > color #1,2/B rgb(0.000,0.831,0.321) > color #1,2/C rgb(1.000,0.861,0.137) > color #1,2/D rgb(1.000,0.400,0.100) > color #1,2/E rgb(0.780,0.000,0.400) > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.82647,-0.51941,0.21716,224.85,-0.53861,0.61724,-0.57351,177.83,0.16385,-0.59096,-0.78989,191.81,#2.1,1,0,0,0,0,1,0,0,0,0,1,0 > color #1,2/A:424-447 green > color #1,2/A:454-518 red > color #1,2/A:348-423 dark orange > show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799@CA target a

2 1

clashes after mutagenesis
by tiger wang 26 Oct '21

26 Oct '21

Dear I am quite new to Chimera. I am using ChimeraX to do some mutagenesis in the protein with its 3D structure. After mutagenesis, the clashes were found. I tried to use tool torsion to adjust the atoms' angles and found when one clash was solved the other clashes came up. It seems it is a endless process. The question is how to correct the clashes due to mutagenesis, only manually adjust one by one using tool torsion or there is other ways to do in the same time simutaneously, such as using modeller inbeded in ChimeraX? Thanks very much for your help Sincerely Tiger Wang

2 2

Refine predicted structure by pulling
by Roden Deng Luo 26 Oct '21

26 Oct '21

Dear ChimeraX Users, There is this AlphaFold prediction: https://alphafold.ebi.ac.uk/entry/P02549. And we know this protein should be more or less in a rod-like shape rather than a globular shape: https://en.wikipedia.org/wiki/Spectrin and related literature such as https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218374/. I wonder is there a way that we can pull the two ends of the predicted structure while maintaining the secondary structures, mostly alpha-helices in this case, inside ChimeraX? I am quite new to ChimeraX. I understand this is more fitted to an MD simulation. But I got to know there are options to fit a PDB to a density map. So I wondered if this can be achieved in ChimeraX. Best, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Re: [chimerax-users] Test files for bug report [ChimeraX] #5467: AmiraMesh
by Tom Goddard 26 Oct '21

26 Oct '21

Hi Roden, These 3 Amira files are vertex/edge/point data, not 3D lattices. The ChimeraX reader only handles 3D lattices Amira files. It does not look like our ChimeraX documentation explains this. I'll try to get this on our docs (3d lattice volume data, float, unsigned 16-bit, uncompressed only). Tom > On Oct 25, 2021, at 12:20 PM, Roden Deng Luo <deng.luo(a)kaust.edu.sa> wrote: > > Dear Tom and Andrea, > > Thanks for the quick responses. Upon the kind approval from Andrea, I attached the .am file I received from Andrea (in the format of 2.0), as well as the other two that are exported from this file (in the format of 3.0, one is in ascii as revealed by the name). > > Best regards, > Roden

2 3

Open AmiraMesh 3.0 in ChimeraX
by Roden Deng Luo 25 Oct '21

25 Oct '21

Dear ChimeraX Users, I have an AmiraMesh .am file exported from Amira 3D 2021.1 (Build date: 2021-06-21 13:21:22, SHA id: 213bd1......13c73e). When I load it into ChimeraX 1.2.5 or ChimeraX 1.3.dev202110231141, ChimeraX tells me the following error. First line of AmiraMesh file must start with "# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", instead got "b'# AmiraMesh BINARY-LITTLE-ENDIAN 3.0\n'" Googling "AmiraMesh site:https://www.rbvi.ucsf.edu/pipermail/chimerax-users" shows no result. Can anyone kindly help here? Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 5

problem with displaying secondary structures
by Elżbieta Wątor 24 Oct '21

24 Oct '21

Hi, I am trying to prepare figures for my publications and I have a problem with ss assignment. When I open structure in pymol, everything is assigned correctly. However, when I open the same structure in ChimeraX (1.2.5) I have gaps in helices and also not all of B strands are assigned correctly. I tried "dssp" command, but I probably type something wrong, because everytime I got "expected keyword" reply. Also I tried to do that manually using such commands setattr /B:5-7 res ss_type 1 and for some regions it works and for some not e.g I can change the whole helices with gaps to loop but in other way around it again gives me back helices with gaps. I've just started learning ChimeraX so probably there is some easy explanation, but I would be really grateful for your help. Best regards, Ela Wator

2 1

red-cyan 3D view in chimera X?
by Maya Shmulevitz 22 Oct '21

22 Oct '21

Hi everyone, Does anyone know how to switch to red-cyan for the structures so that my class can see them with 3D red/cyan glasses? I used to do it on the old chimera with the camera feature but cannot find the option in chimera X. Thank you!! -- Maya Shmulevitz Canada Research Chair in Molecular Virology and Oncotherapy Associate Professor University of Alberta Medical Microbiology and Immunology Li Ka Shing Institute for Virology 6-21 HMRC Edmonton, Alberta, T6G 2E1 CANADA

3 3

Running ChimeraX and a REPL
by Tom Mulvaney 21 Oct '21

21 Oct '21

Hi all, I'm wondering if anyone has any experience running ChimeraX with either a standard REPL or IPython REPL? ChimeraX already has a 'shell' tool that allows interacting with ChimeraX through a Python REPL which I've found invaluable for testing out ideas and poking around in ChimeraX in general. It would be really nice though if I could send Python code directly from my IDE to be evaluated. In order to make this work, it would be great if ChimeraX could be run from a terminal and provide a Python (or preferably IPython) REPL. As it stands, I've managed to nearly make this work with the following script: import IPython.terminal.embed IPython.terminal.embed.embed() I then run: ChimeraX --script repl.py After typing, `%gui qt5`, the ChimeraX GUI appears. I can then interact with the REPL directly from the comfort of Emacs and evaluate things - but! - the main 3D view does not end up being displayed. Does anyone know how to get the REPL and 3D stuff to work side-by-side? Kind regards, Tom

3 3

ChimeraX issue
by Amaya Cuesta, Joan 20 Oct '21

20 Oct '21

Dear ChimeraX Team, I'm trying to use ChimeraX on my VM (Ubuntu 20.04.01), but I'm having the error on the screenshot attached below. I tried to update OpenGL to 3.3, and on the terminal it seems that it installed everything but then when I try to open again I'm getting the same issue. I tried to update OpenGL following this: https://www.reddit.com/r/Ubuntu/comments/8tpq05/how_can_update_my_display_d… But always when I do the command: glxinfo | grep "OpenGL version" , it shows: "OpenGL version string: 3.1 Mesa 21.0.3". Not sure why it is not updating to 3.3 while all the other packages are upgraded. Could you please advice? Kind regards Joan Cuesta (BSc) Viral Zoonoses Research Scientist Rabies and Viral Zoonoses Group Animal & Plant Health Agency (APHA) Internal extension: 71528 External: 02087201528 | Email: Joan.Cuesta(a)apha.gov.uk<mailto:Joan.Cuesta@apha.gov.uk> Website: www.gov.uk/apha<http://www.gov.uk/apha> | Twitter: @APHAgovuk<http://www.twitter.com/aphagovuk> | Facebook: aphagov<http://www.facebook.com/aphagov> Address: APHA Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK Working hours - Monday - Friday, 9 - 5:30 pm Department for Environment, Food and Rural Affairs (Defra) This email and any attachments is intended for the named recipient only. If you have received it in error you have no authority to use, disclose, store or copy any of its contents and you should destroy it and inform the sender. Whilst this email and associated attachments will have been checked for known viruses whilst within Defra systems we can accept no responsibility once it has left our systems. Communications on Defra's computer systems may be monitored and/or recorded to secure the effective operation of the system and for other lawful purposes.

4 5

I Have a Problem Installing ChimeraX on Debian Buster
by Stephen P. Molnar 20 Oct '21

20 Oct '21

I am attempting the installation of ChimeraC-1.2.5(chimerax-1.2.5-rc-2021.05.24) on my up to date Debian v-1064 bit platform. I open the tar.gz package without any difficulties, but when I attempt to execute ChmieraX i get the following: comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ ./ChimeraX qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb. Fatal Python error: Aborted Current thread 0x00007fcb3dafd740 (most recent call first): File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__ File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module> File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 87 in _run_code File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 194 in _run_module_as_main Aborted comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ xcb is installed, but the Debian v-10 default version of python is 3.7. Is this the problem? Is there a solution? Reinstalling did not fix the problem. Thanks in advance. -- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

2 1

Remote Desktop usage
by Dmitry Semchonok 20 Oct '21

20 Oct '21

Dear colleagues, What could be the solution for the remote desktop of Chimera X user? One of the solution can be VNC but is there any other? Thank you Sincerely, Dmitry

2 1

coil thickness
by Lisandro Otero 18 Oct '21

18 Oct '21

Dear Chimera developer; How can I change the coil thickness in a specific loop in ChimeraX? I have tried with the Hierarchical Specifiers but I was unsuccessful? Could you please give me a command line as example? I'm using “cartoon style coil thickness XX” Thanks in advance. Best. Dr. Lisandro H. Otero PhD. Leloir Institute Foundation Av. Patricias Argentinas 435 C1405BWE Buenos Aires, Argentina Phone: +054-11-5238-7500 ext. 2552 Fax: +054-11-5238-7501

2 1

Feature suggestion - Models panel
by William Hofsøy 18 Oct '21

18 Oct '21

Hi, I would like to suggest/request that the "Models" panel should be able to rename models and change their ids from the list of models directly either through double click, like changing file names on windows, or through the right click context menu. Best regards, William

2 1

Re: [chimerax-users] labelling hbond atoms
by Rangarajan, Amith 14 Oct '21

14 Oct '21

Dear Group, I have a possibly rookie level question. When i use name flag with hbonds command to define two groups of hbonds like this hbonds (#1.1 & protein) restrict (#1.2.* ) distslop .2 reveal t rad .2 color gold name HBONDS-1 hbonds(#1.1 & ~protein) restrict(#1.2.*) distslop .2 reveal t rad .2 color magenta name HBONDS-2 then when i try to label the hbond atoms , la hbondatoms residues font "Rockwell Extra Bold" height .6 bg 20,20,20 I am not getting the labels. I am not getting any errors so i figured that it got to do with hbonds being given a name , however i am not able to fix this. welcome to hear your suggestions. thanks again., amith

3 2

ProblemI am attempting he installation of ChmimeraX Installing ChimeraX on Debian mv-10
by Stephen P. Molnar 14 Oct '21

14 Oct '21

I am attempting the installation of ChimeraC-1.2.5(chimerax-1.2.5-rc-2021.05.24) on my up to date Debian v-1064 bit platform. I open the tar.gz package without any difficulties, but when I attempt to execute ChmieraX i get the following: comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ ./ChimeraX qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb. Fatal Python error: Aborted Current thread 0x00007fcb3dafd740 (most recent call first): File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__ File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module> File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 87 in _run_code File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 194 in _run_module_as_main Aborted comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ xcb is installed, but the Debian v-10 default version of python is 3.7. Is this the problem? Is there a solution? Reinstalling did not fix the problem. Thanks in advance. -- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

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Question about pruned set in rmsd
by Chang Jang 14 Oct '21

14 Oct '21

Hi Chimera Users, I want to understand a result from "match" command. There are two results for 1) pruned set and 2) across all. What exactly is the pruned set in this calculation? Thanks, Chang Woon Jang

2 1

Use values printed from Log inside a script (e.g. RMSD)
by Steven Truong 12 Oct '21

12 Oct '21

Dear ChimeraX Admins, I was hoping to use the “rmsd” command in ChimeraX to measure distances between models within a .py script. Is there a way to use the output of “rmsd” (or generally any other output in Log) within the script? For example, if rmsd > 2 Angstroms, then do X. Ultimately, I am attempting to align chains between models. Because my protein is asymmetric, chain A on Model #1 might actually be chain B on Model #2. I was hoping to use “rmsd” to map one chain to the other. Is it a better idea to do this in another program and re-write chain IDs in the .PDB file? If so, what other program would be better at making RMSD calculations between .PDB chains? Thank you, Steven Truong Cambridge University

4 10

Electrostatic color key problem
by Luca Pellegrini 12 Oct '21

12 Oct '21

Hi, Coloring a surface with ‘electrostatic’ in the ‘Molecule display’ works fine. However, when I try to modify the red-blue boundary values from the default -10, 10 in the color key box, the surface color doesn’t seem to change. Can you please advise? Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

2 3

fold
by Ruggero Gabbrielli 11 Oct '21

11 Oct '21

Maybe it’s a little too early for that, but can’t you just add a button for folding a sequence?

2 1

"fly" interrupting "turn"
by Anderson, Jacob 11 Oct '21

11 Oct '21

Dear ChimeraX Users, Making a movie with a CXC script/command file, I find that the "fly" command interrupts the "turn" command. For example if I run these two lines: turn y 0.25 1440 fly Frame_01 400 Frame_02 400 Frame_03 400 Frame_04 400 Frame_05 Before the turn completes, the view goes to Frame_01. Is this the expected behavior? If not, would love any tips on how to complete a turn of the molecular model before flying to Frame_01 (or p1 in the ChimeraX fly user help documentation). Jacob

2 1

Re: [chimerax-users] Measuring Colocalisation using ChimeraX
by Tom Goddard 08 Oct '21

08 Oct '21

Hi Dominic, Ok, here is a way to do what you described that does not need any Python. First you place a marker at the enter of the green blob using ChimeraX Markers toolbar using the Center mode (mark center of connected surface). Once you select that mouse mode, right click on the green blob to place the marker. Then make a sphere centered at that marker with the shape command, e.g. "shape sphere center #3 radius 100". Then mask the red map to get just the part inside that sphere, e.g. "volume mask #1 surface #4". Then measure the volume enclosed in that masked map surface, e.g. "measure volume #5". You might also be interested in exactly how much red blob is inside the green blob and you could mask the red using the surface of the green to do that. Tom > On Oct 8, 2021, at 2:33 AM, BINGHAM Dominic <dominic.BINGHAM(a)univ-amu.fr> wrote: > > The custom python code sounds more applicable to what I am doing. I will give that a try but also would greatly appreciate some tips > > > To give context, I have several maps like shown above, with 2-channels showing the staining of one protein each. Each map is a synapse, and these are taken from 3D-STORM images contains several synapses. I have 3 different conditions, and I would like to compare what I measure and how it changes between these conditions. So for instance, ideally, what I would like to do is to measure from the centre of the large green structure which is colocalised to the large red structure (Circle on image above). I would then like a value to represent the relative amount of the ‘red’ protein within a set volume around the ‘green’ structure. I would then compare this value between each condition. > > So any tips on the code for python would be great here! > > Thanks so much for the help! > > Dominic > >> Le 6 oct. 2021 à 20:08, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> a écrit : >> >> Hi Dominic, >> >> The ChimeraX Distances tools measures distances between atoms in an atomic structure. You have image data, not an atomic structure so that is why it will not report any distances. >> >> One way to proceed would be to place a marker on every connected surface piece in each of the two images, then measure distances between these centroid markers. There is code to place the markers using ChimeraX here >> >> https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html <https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html> >> >> Markers are treated just like atoms in ChimeraX so the Distance tool would work. But you want all nearby distances so you might try the Contacts tool >> >> https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> >> >> That may not give you what you want. Very likely you would need to write some custom Python code to get exactly what you want. Probably you also want the volume enclosed in each blob. If you need tips on how to write that Python code I can advise if you give specifics of what you want. >> >> Tom >> >> >> >> >> >> >>> On Oct 6, 2021, at 4:11 AM, BINGHAM Dominic via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hello, >>> >>> I have a problem with which I’m trying to use chimeraX to solve. I have some images of synapses with which I have super-resolved two proteins in 3D (so two images/channels). I want to quantify the colocalisation of a structure of one protein to the blobs of the other protein within a certain distance. Shown below is the non-segmented map of the 2 images of proteins. So for example I would want to quantify the colocalisation of the red blobs within a certain distance of specific larger green blobs. I want to then compare these between different conditions. >>> <Capture d’écran 2021-10-06 à 12.58.42.png> >>> >>> I have segmented the images already using "segmentat map ». I have been trying to start with the « distance » tool to measure how far one blob of protein is from the structure (Image shown below of two selected structures in just the map of one protein to practice). >>> >>> <Capture d’écran 2021-10-06 à 12.57.28.png> >>> >>> However, this doesn’t seem to work functionally as no distance is shown when I try to perform the function. Also, this function may possibly be too basic for what Im trying to do. That said, any help on how to use this function would still be greatly appreciated. >>> >>> >>> Ultimately, I think the best thing for what I would like is to be able to select a specific structure and have a measurement of all the blobs of the other protein within a defined 3D radius of this structure, and then compare this value between different conditions. I have been looking through the user manual and I can’t seem to find anything that will do something like this… I (and my PhD) would be monumentally grateful if you could possibly help me with this problem? Either by pointing me to the correct function, or even a thread that has discussed a similar problem that I may have missed? >>> >>> >>> Thanks and have a wonderful day, >>> >>> Dominic Bingham >>> PhD student at Aix-Marseille University >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >> >

1 0

hbonds display problem
by Maciej Basczok 08 Oct '21

08 Oct '21

Dear Expert, at the beginning would like to thank you for developing such a wonderful tool as ChimeraX is! I have one problem, namely, when hbonds calculation is run on an RNA molecule with an option to display as pseudobonds, there are many hbonds detected, but displayed are only two of them. Do I keep doing something wrong? I would be very grateful for your help. Kind regards, Maciek

2 6

polishing video
by Ruchika Bajaj 07 Oct '21

07 Oct '21

Hi Elaine Hope you're doing well !! I need to polish my videos. I am mainly using the following commands. I am just wondering if you have any more suggestions to improve the quality of the movie. Please let me know. I would appreciate your help in this regard. Thanks !! Regards Ruchika set bgColor white; lighting simple; graphics silhouettes true; lighting soft movie record supersample 3; movie encode quality higher

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Re: [chimerax-users] Error on installing isolde
by benhaijing＠sina.com 07 Oct '21

07 Oct '21

Hi Greg!Thanks very much! After I deleted the two directories: (1) site-packages\ChimeraX_UI-1.2.1.dist-info and (2) site-packages\chimerax\ui in my computer, I have successfully reinstalled chimerax and isolde! It works now!Best regards, Haijing Ben ----- 原始邮件 ----- 发件人：Greg Couch <gregc(a)cgl.ucsf.edu> 收件人：benhaijing(a)sina.com, chimerax-users <chimerax-users(a)cgl.ucsf.edu> 主题：Re: [chimerax-users] Error on installing isolde 日期：2021年09月28日 06点24分 Actually, it worse than I thought. Uninstalling the user-installed version of the UI bundle is not doable from within ChimeraX. And uninstalling ChimeraX and reinstalling it doesn't help, because that only takes care of system files, not any of the user's customization. To get rid of the user installed bundle, the first step is to find where on the filesystem the files are. So start the Shell tool from the Tools / General menu. And then type in it: import chimerax chimerax.app_dirs.user_data_dir That will show where to go. For example, for me on Windows, it prints: 'C:\\Users\\gregc\\AppData\\Local\\UCSF\\ChimeraX\\1.2' So using the Windows file brower, I would navigate to C:\Users\gregc\AppData\Local\UCSF\ChimeraX\1.2. You may need to check "Hidden Items" in the View menu to navigate into AppData directory. macOS and Linux users should have an easier time going to the correct directory. And they would use forward slash, /, instead of backslash, \. The next step is to remove two directories: (1) site-packages\ChimeraX_UI-1.2.1.dist-info, and (2) site-packages\chimerax\ui. And then, when you restart ChimeraX, you'll be back to the version that came with ChimeraX. HTH, Greg On 9/27/2021 2:22 PM, Greg Couch via ChimeraX-users wrote: Hi Haijing, The output you pasted says that ISOLDE is already installed, so you don't need to install it again. It should be reinstallable, so that is a bug. If you use the graphical toolshed interface (click on More Tools... in the Tools menu), you would have seen that the install button for ISOLDE said Installed, meaning it is already installed. In this particular case, it looks you made things worse by deliberately installing an older version of the UI bundle from the toolshed than the version that came with ChimeraX. Using the graphical toolshed interface, you would have seen that it was a downgrade, which means do not install it unless necessary. Or maybe you used the Updates tool to do that? If so, you should have seen that installed version was 1.7.6 and the version on the toolshed is 1.2.1, so much older. Regardless of how you did it, to fix it, give the command: toolshed uninstall ui And that should revert back to version of the UI bundle that came with ChimeraX. The fact that you could install an older, incompatible, version of the UI bundle is a bug that is difficult to fix in the general case. Best regards, Greg On 9/26/2021 5:55 PM, benhaijing--- via ChimeraX-users wrote: Hi all！ I can’t install the plugin isolde using command 'toolshed install isolde'. Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Requirement already satisfied: ChimeraX-ISOLDE==1.2.2 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (1.2.2) Requirement already satisfied: ChimeraX-AtomicLibrary~=3.1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (3.1.3) Requirement already satisfied: ChimeraX-Core~=1.2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.2.5) Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-Clipper~=0.16.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-ISOLDE==1.2.2) (0.16.0) Requirement already satisfied: ChimeraX-Atomic~=1.13.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.13.2) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0.1) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.3) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0) Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.4.1) Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ConnectStructure~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.5) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.4) Requirement already satisfied: ChimeraX-IO~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-UI~=1.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.2.1) INFO: pip is looking at multiple versions of chimerax-pdblibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-pdb to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-opencommand to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-nucleotides to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-io to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-dataformats to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-mmcif to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-graphics to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-geometry to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-core to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomsearchlibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-connectstructure to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-clipper to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomiclibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomic to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-arrays to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-isolde to determine which version is compatible with other requirements. This could take a while. The conflict is caused by: chimerax-nucleotides 2.0.1 depends on ChimeraX-UI~=1.0 chimerax-opencommand 1.5 depends on ChimeraX-UI~=1.0 chimerax-savecommand 1.4 depends on ChimeraX-UI~=1.4 To fix this you could try to: 1. loosen the range of package versions you've specified 2. remove package versions to allow pip attempt to solve the dependency conflict ERROR: Cannot install chimerax-nucleotides==2.0.1, chimerax-opencommand==1.5 and chimerax-savecommand==1.4 because these package versions have conflicting dependencies. ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies WARNING: You are using pip version 21.0.1; however, version 21.2.4 is available. You should consider upgrading via the 'C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip' command. Thanks, Haijing Ben _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

1 0

Mol2 file conversion
by Marcus Agyin 06 Oct '21

06 Oct '21

Hello, I am emailing to get clarification on how I would convert a chimera file into a Mol2 file. If I’m understanding correctly, I would need to click on “File” and in the pop-up menu there would be a “save as Mol2” option, however, all that it is showing the generic “Save” option. Thanks in advance, Marcus Agyin

2 1

Measuring Colocalisation using ChimeraX
by BINGHAM Dominic 06 Oct '21

06 Oct '21

Hello, I have a problem with which I’m trying to use chimeraX to solve. I have some images of synapses with which I have super-resolved two proteins in 3D (so two images/channels). I want to quantify the colocalisation of a structure of one protein to the blobs of the other protein within a certain distance. Shown below is the non-segmented map of the 2 images of proteins. So for example I would want to quantify the colocalisation of the red blobs within a certain distance of specific larger green blobs. I want to then compare these between different conditions. [cid:5E6B5354-093F-44B8-BCD8-9C01AFDEAF72] I have segmented the images already using "segmentat map ». I have been trying to start with the « distance » tool to measure how far one blob of protein is from the structure (Image shown below of two selected structures in just the map of one protein to practice). [cid:ED6171EE-E03F-47C8-A3AE-81A7E5FC9177] However, this doesn’t seem to work functionally as no distance is shown when I try to perform the function. Also, this function may possibly be too basic for what Im trying to do. That said, any help on how to use this function would still be greatly appreciated. Ultimately, I think the best thing for what I would like is to be able to select a specific structure and have a measurement of all the blobs of the other protein within a defined 3D radius of this structure, and then compare this value between different conditions. I have been looking through the user manual and I can’t seem to find anything that will do something like this… I (and my PhD) would be monumentally grateful if you could possibly help me with this problem? Either by pointing me to the correct function, or even a thread that has discussed a similar problem that I may have missed? Thanks and have a wonderful day, Dominic Bingham PhD student at Aix-Marseille University

2 1

Hidden points present in gltf file
by Scott, Brandon L. 06 Oct '21

06 Oct '21

I'm having an issue with gltf exporting with hidden objects. The surface that is exported looks correct; however, when querying the points in the exported file all the hidden ones are there as well which is hindering a downstream analysis. Exported gltf: [cid:18a58daf-6676-4fe8-ab6c-935e631e379d] Rendered points from gltf: [cid:3bd25148-70ad-4079-885b-368e0d2c57af] Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor Nanoscience & Nanoengineering South Dakota Mines 501 E. Saint Joseph St., Rapid City, SD 57701 724.510.1253 | Brandon.Scott(a)sdsmt.edu<mailto:Brandon.Scott@sdsmt.edu> [South Dakota Mines]<https://www.sdsmt.edu/> [South Dakota Mines on Facebook]<https://www.facebook.com/SouthDakotaMines/>[South Dakota Mines on Instagram]<https://www.instagram.com/southdakotamines/>[South Dakota Mines on Twitter]<https://twitter.com/sdsmt>[South Dakota Mines on Snapchat]<https://www.snapchat.com/add/sdsmt>

2 1

Error messages when executing command file with chimerax --exit
by Guillaume Gaullier 05 Oct '21

05 Oct '21

Hello, When I run the attached command file from within ChimeraX 1.2.5 on macOS 10.15.7 (open 7otq_figure-2-supplement-2.cxc), it completes without any error. However, when I run it from the shell with 'chimerax --exit 7otq_figure-2-supplement-2.cxc', I get the attached errors in the terminal. In both cases, the figures are generated correctly, so as far as I am concerned it seems I can simply ignore these errors. But I thought you (ChimeraX developers) might need to know that this happens. This does not happen with other command files (I have been happily making movies without ever seeing these error messages), which makes me think maybe the problem is specific to this particular one? Cheers, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

3 3

Structure Prediction on ChimeraX
by Chang Jang 04 Oct '21

04 Oct '21

Hi ChimeraX users, I am trying to find Structure Prediction -> AlphaFold but there seems no such tool. Would you please guide me on how to add the "Structure Prediction" tool on ChimeraX? Thank you. Best regards, Chang Woon Jang

2 1

can isolde work with ChimeraX 1.3 developer versions?
by Sindelar, Charles 04 Oct '21

04 Oct '21

Hi all, any chance I can persuade ChimeraX v1.3 (i.e. nightly downloads) to use the current version of Isolde? I would love to use some of the newest features of ChimX together with Isolde, but the toolshed does not allow this (says only ChimX 1.2 is allowed). Are they really incompatible? Can I perhaps "trick" the toolshed somehow? Thanks for all your work to make these fabulous tools. By the way, Tom, Eric, Elaine and team, I *love* the new tool-switching shortcuts, i.e. shift-esc and control-tab. They make my life so much easier and this is a primary motivation for my request (but other new features in 1.3 also). Cheers! Chuck --------------------- Charles V. Sindelar, Ph.D. Dept. of Molecular Biophysics and Biochemistry Yale University Bass 335 New Haven, CT 06520-8114 Lab (203) 432-3095 Fax (203) 432-5175 http://medicine.yale.edu/mbb/faculty/charles_sindelar.profile

3 2

crossfade command not working from a command file
by Guillaume Gaullier 01 Oct '21

01 Oct '21

Hello, I am using ChimeraX version 1.2.5 (2021-05-24) on macOS 10.15.7. When trying to generate a simple movie with the attached command file, I get the attached wrong result in which the crossfade command seems to fail (instead of a smooth transition, I only get a flashing black screen for a few frames). A similar problem happens with the same version of ChimeraX on Rocky Linux 8.4. Instead of loading the command file from a fresh session (with 'open command-file.cxc'), I tried to prepare my models first, and then sent the commands generating the movie all at once (separated by semi-colons). When I did it this way, I got the correct result (also attached). Is there anything I am doing wrong, or is this a bug? I am pretty sure the command file version worked correctly in a previous version of ChimeraX, because I have done this before. Unfortunately, I don’t remember which version it was (but probably 1.1, since it was just last year). I would appreciate any help with this. Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

3 6

Tiling images are stepped
by Pranav Shah 30 Sep '21

30 Sep '21

Hi, I want to create an image of multiple volumes that are tiled horizontally. However, when I run the command "tile columns 6" the volumes get arranged in a step-like manner (attached image). I do not see this happen in chimera so I am wondering if this expected behaviour in ChimeraX? I am on UCSF ChimeraX version: 1.2.5 (2021-05-24) on the M1 MacBookPro, MacOS 11.6. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

3 3

Syncing up the movement of "plane" volumes.
by Mayer, Megan 30 Sep '21

30 Sep '21

Hi ChimeraX community. I have a reconstructed tomogram which has 92 ‘Z’ slices, and a segmentation volume that has ‘374’ slices. They are both displayed as “Plane” in the volume viewer (image attached). I would like to record a movie where they are showing the same features simultaneously. I have used the command: “volume #5 planes z,0,92; volume #2 planes z,0,374 ; wait 120 ; “ However, the volumes do not move at the same time: volume 5 completes before volume 2 begins. Is there a way around this, so that I can play both volumes at the same time? Thank you for any tips! Megan

2 2

adding new trajectory format
by Radosław Giziński 30 Sep '21

30 Sep '21

Hi, Is there a way I can add custom, multi-frame trajectory format to ChimeraX so I can view multi frame trajectories? Is there some manual that could guide me through the process like this?: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html (scroll to the bottom) Best regards, Radosław Giziński

3 2

movie encode bug on Rocky Linux 8.4
by Guillaume Gaullier 30 Sep '21

30 Sep '21

Hello, This time I am reporting what looks almost certainly like a bug. Using ChimeraX version 1.2.5 on Rocky Linux 8.4 (installed from the RHEL/CentOS 8 RPM package), I get the following error in the Log when trying to use the movie encode command (I attached a copy of the full error message in the Log): /usr/libexec/UCSF-ChimeraX/bin/ffmpeg: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory Turns out I definitely have libbz2 on my system, but not under the filename ChimeraX (or ffmpeg bundled with ChimeraX) is looking for: $ ls -l /usr/lib64/ | grep libbz2 lrwxrwxrwx. 1 root root 11 Apr 7 03:44 libbz2.so -> libbz2.so.1 lrwxrwxrwx. 1 root root 15 Apr 7 03:44 libbz2.so.1 -> libbz2.so.1.0.6 -rwxr-xr-x. 1 root root 73008 Apr 7 03:44 libbz2.so.1.0.6 If I create a symlink to libbz2.so.1.0.6 and name it libbz2.so.1.0, my movie encode command finishes fine and produces a movie file. So it was easy to work around this problem, but obviously it would be a lot better if it worked out of the box and the user did not have to mess with system files as root. Thank you in advance, Guillaume N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

3 3

Trackpad scaling causes unintended rotation
by Oliver Clarke 29 Sep '21

29 Sep '21

Hi, In recent versions of ChimeraX (I don't think it always did this but can't be 100% sure), when one uses pinch-to-zoom on the trackpad to scale the view, this also changes orientation, causing quite a large and unintended rotation which can be a bit disconcerting. Comparing directly with Chimera using the same model, this does not happen in Chimera. Is there some difference in how the Chimera vs X are interpreting competing trackpad gestures, and could this be adjusted in ChimeraX? Because two fingers can be used both to scale and rotate... Chimera seems to be able to figure out which the user is intending, while ChimeraX presently applies both at the same time. Cheers Oli

3 6

Possible to measure the shortest distance between two models?
by Vorländer,Matthias Kopano 28 Sep '21

28 Sep '21

Dear all, I am interested in measuring the shortest distance between two models (PDBs) without a priori knowledge of which atoms will be the closest ones. I am planning to do this for a large number of model pairs, therefore it would be great if this would be scriptable. Is this possible using ChimeraX? Thanks a lot in advance, Best, Matthias

3 6

Have a map move with its model
by Bullitt, Esther 28 Sep '21

28 Sep '21

Hi, I renamed my map and model to be #9.1 and #9.2, thinking this would make them move together. However, when I used matchmaker to match the model to align it to another model, only the model moved and the map did not. To start with, I used fitmap #9.1 inMap #9.2, but now the model is elsewhere. If I go back and do fitmap again, it moves the wrong thing (I want to put the map where the model is now, not vice versa). Is there something I am missing, or is there a different way to do this? Thanks very much. Sincerely, Esther

2 1

Flat transparency setting absent
by David William Kastner 27 Sep '21

27 Sep '21

ChimeraX community, I noticed that in ChimeraX, the “flat” transparency option that was present in Chimera has been either moved or renamed in ChimeraX. This setting made it so the transparency setting wasn’t overwhelming/distracting when focusing on details. In Chimera, it is accessed with Tools > Viewing controls > Effects > transparency > flat. Does anyone know how to achieve this effect in ChimeraX? I find the default ChimeraX transparency option to be disorienting when visualizing details. Here is a rendering comparing the two rendering styles with and without “flat” option. I look forward to your thoughts! https://www.dropbox.com/s/xrjyjnzegeeltap/transparency_comparison.png?dl=0 David --- David Kastner Ph.D. student | Bioengineering MIT | Kulik Lab kastner.io

2 5

Error on installing isolde
by benhaijing＠sina.com 27 Sep '21

27 Sep '21

Hi all！ I can’t install the plugin isolde using command 'toolshed install isolde'. Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Requirement already satisfied: ChimeraX-ISOLDE==1.2.2 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (1.2.2) Requirement already satisfied: ChimeraX-AtomicLibrary~=3.1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (3.1.3) Requirement already satisfied: ChimeraX-Core~=1.2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.2.5) Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-Clipper~=0.16.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-ISOLDE==1.2.2) (0.16.0) Requirement already satisfied: ChimeraX-Atomic~=1.13.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.13.2) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0.1) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.3) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0) Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.4.1) Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ConnectStructure~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.5) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.4) Requirement already satisfied: ChimeraX-IO~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-UI~=1.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.2.1) INFO: pip is looking at multiple versions of chimerax-pdblibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-pdb to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-opencommand to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-nucleotides to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-io to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-dataformats to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-mmcif to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-graphics to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-geometry to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-core to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomsearchlibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-connectstructure to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-clipper to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomiclibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomic to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-arrays to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-isolde to determine which version is compatible with other requirements. This could take a while. The conflict is caused by: chimerax-nucleotides 2.0.1 depends on ChimeraX-UI~=1.0 chimerax-opencommand 1.5 depends on ChimeraX-UI~=1.0 chimerax-savecommand 1.4 depends on ChimeraX-UI~=1.4 To fix this you could try to: 1. loosen the range of package versions you've specified 2. remove package versions to allow pip attempt to solve the dependency conflict ERROR: Cannot install chimerax-nucleotides==2.0.1, chimerax-opencommand==1.5 and chimerax-savecommand==1.4 because these package versions have conflicting dependencies. ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies WARNING: You are using pip version 21.0.1; however, version 21.2.4 is available. You should consider upgrading via the 'C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip' command. Thanks, Haijing Ben

3 3

Compound Docking in UCSF Chimera
by Ayush Patel 25 Sep '21

25 Sep '21

Sir or Madam; Recently, I was having issues with docking a ligand into a receptor due to surface calculation failures. A quick search told me to use ChimeraX. However, I am not sure how to carry out docking in ChimeraX. Could you please explain how to do this? As a side note, I do currently have AutoDock Vina. Thank you so much, Ayush Patel

2 1

Hi. I have a question about Chimera X program
by dongyoung kim 24 Sep '21

24 Sep '21

Hi. I'm researching protein 3D structure to develop the new drug. In recent, I'm using the Alphafold function in Chimera X daily version. I have 4 questions. First, if I use Alphafold to predict my important project data, is it keep secure privately? I want to keep my data secret. It shouldn't be open to anybody without me. Second, when I using Alphafold in ChimeraX, I faced some error messages that mean 'Not enough disk volume. please remove past data.'. I'm not familiar with google colab...how can I manage the disk to remove past data or expand disk volume? Third, how can I improve the speed of alphafold prediction? ChimeraX shows some resources like ram, disk. fourth, I want to operate simultaneously Alphafold prediction to predict 2 or more structures. Is it possible? If there need some pay to improve the second, third, fourth question, please let me know methods. Many thanks. -from KDY

3 2

Finding Continuous Residue Stretches
by Daniel Wells 23 Sep '21

23 Sep '21

Dear Chimerax Users: I need to find Continuous Residue Stretches between 15-25 amino acids in length on the surface of these two molecules: https://www.rcsb.org/3d-view/4MYV/1 https://www.rcsb.org/structure/3U82 Could anyone here help me perform that function on Chimerax? Thank you for your time. Sincerely, Dan Wells

2 1

Error on save
by Christophe Leterrier 23 Sep '21

23 Sep '21

HI, When I'm saving a session displaying 3D image stacks as surfaces into a csx file, I get this error: TypeError: object of type 'SurfaceUpdaters' has no len() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 242, in discovery if sm is None and len(value) == 0: However if I switch the displayed stacks as volume, then there is no error on save. This is with the daily build 1.3.dev202109160803 (2021-09-16) on OSX Big Sur (Intel architecture). Thanks, Christophe

3 3

A couple questions about programming in ChimeraX
by William Hofsøy 22 Sep '21

22 Sep '21

Hi, I'm currently working on a plugin that deals with a cmm-file model and have a few questions about how to do certain things. Mainly I would like to be able to modify the model by adding new markers and links to the model. I have managed to figure out how to make new markersets and add them to the session but not how to alter existing ones aka the model that I load from the cmm file. Additionally I am making use of the marker_extra_attributes info since the cmm file im reading has attributes there that I need, but as I read in the documentation these aren't saved in sessions and I wondered if there is a way to do just that. Lastly, I was wondering if it is possible to place any mesh in the scene, for instance a cube. -William

2 3

Re: [chimerax-users] Adding a custom preset question
by Elaine Meng 22 Sep '21

22 Sep '21

Hi Boaz, Just download the file using your standard browser mechanism. When I ctrl-click on the link "kyte-doolittle_hydrophobicity.cxc" in this page: <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup> ...when viewed in Firefox on Mac, I get a menu that includes "Save link as..." Choosing that brings up a little dialog that I use to save the file (without changing the name, but you can change it if you keep the cxc part) to my desired download location. On other platforms or different browsers it might be slightly different how to get the context menu with the choice to save the file, but should be similar. Or since it is a plain text file, like you said, you can also view contents and then paste them as plain text in a text-editor to create your own cxc file. However it is usually easy just to save the file from the browser as described above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 21, 2021, at 10:13 PM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi, > You give a nice example of adding the kyte-doolittle_hydrophobicity.cxc to the custom_presets folder that I created, but where can I find this file? Or, should I paste the content of the file which is opened by pressing the link in the user guide into a file by this name ( I doubt it but nevertheless suggest it as a possibility). > Excuse my naive question, please. > Thanks, > Boaz

1 0

color zone colors by atom type
by vincent Chaptal 21 Sep '21

21 Sep '21

Dear ChimeraX users, I just subscribed so apologies if this has been asked before. When is type the command: color zone #2 near #1/A distance 5 sharpEdges false farColor blue I have the volume #2 in blue with chain A colored by atom type: i.e. with carbons in sand, oxygens in red, nitrogens in blue. I tried to follow the tutorial on youtube, downloading the model and emdb like in the tutorial, and it does work like the tutorial, meaning colored by chain. I am wodering what is going on and how to fix it? I've seen this behavior for my protein, on a PDB refined from Phenix, or from a download from the rcsb. I don't see anything special on the PDB, all the atoms are listed normally. Is it possible to assign a specific color per chain using this command? Thank you for your help. best Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

2 3

Download Speed
by Gulzar Singh 21 Sep '21

21 Sep '21

Dear Chimera Teach team, The download speed of software is less than 200KB/s (mostly 160 KB/s). I tried both Firefox and wget. We have download limit of 11MB/s My location is Pune, India Please have a look at the issue. Regards, Gulzar Singh

2 1

Turning off silhouettes to specific selection
by Abhilash Padvannil 17 Sep '21

17 Sep '21

Hi Is there a way to turn off the silhouettes on specific selections of a model? Thanks Abhilash.

2 1

Remove older ChimeraX Linux
by Nebojsa Bogdanovic 16 Sep '21

16 Sep '21

Hello, I am trying to reinstall the new ChimeraX on the linux system, however my previous incomplete installations are creating problems. I am not sure how to get rid of them and start anew so I would appreciate your help. I can send more context in our next correspondence. Looking forward to hearing from you. Thank you and best regards. Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

2 1

Interface residue selection - command line option?
by Vorländer,Matthias Kopano 15 Sep '21

15 Sep '21

Dear ChimeraX team, I am trying to selected interface residues using the “interface” tool. While doing this through the context menu of the interface plot works, I am analyzing a larger number of PDBs and am therefore looking for a way to achieve this through the command line (the contacting chains are displayed already in the log window. Essentially I wonder if it is possible to expand this to the contacting residues). Thanks a lot in advcance, Matthias

3 4

how to save .pdb file of predicted fusion protein generated by chimerax and alphafold
by Ruby Pelingon 15 Sep '21

15 Sep '21

Hi, I tried using chimeraX and alphafold to predict my fusion protein. The result seems promising and generated a .pdb file. I would like to enquire how to save the .pdb file. I would like to open the .pdb file using pymol. Thank you. Kind Regards, Ruby Pelingon

2 2

Re: [chimerax-users] [ChimeraX] #5218: surface color value on mouseover replaced by chain info in status line
by Elaine Meng 15 Sep '21

15 Sep '21

Hi Boaz, When a bug is reported as fixed, the next successful daily build should contain the fix. Occasionally the fixer might forget to do all the steps to get it in that day, but it is supposed to be in there. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 15, 2021, at 8:14 AM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi Tom, > Thanks a lot. Is this fix already implemented in the Chimerax daily build? > Cheers, > Boaz > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben Gurion University > Beer Sheva, Israel > > On 14 Sep 2021 17:26, ChimeraX <ChimeraX-bugs-admin(a)cgl.ucsf.edu> wrote: > #5218: surface color value on mouseover replaced by chain info in status line > ----------------------------------+------------------------- > Reporter: Elaine Meng | Owner: Tom Goddard > Type: defect | Status: closed > Priority: high | Milestone: > Component: UI | Version: > Resolution: fixed | Keywords: > Blocked By: | Blocking: > Notify when closed: | Platform: all > Project: ChimeraX | > ----------------------------------+------------------------- > Changes (by Tom Goddard): > > * status: assigned => closed > * resolution: => fixed > > > Comment: > > Fixed. > > Made surface value status message suppress chain description status > messages on mouse hover. > > -- > Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5218#comment:3> > ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> > ChimeraX Issue Tracker > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

1 0

Fwd: Display of actual values of APBS electrostatic potential projected on protein surface
by Boaz Shaanan 13 Sep '21

13 Sep '21

Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel ---------- Forwarded message ---------- From: בעז שאנן <bshaanan(a)bgu.ac.il> Date: 9 Sep 2021 17:39 Subject: Display of actual values of APBS electrostatic potential projected on protein surface To: ChimeraX-users-request(a)cgl.ucsf.edu Cc: Hi, Is there a way in Chimerax to know the actual APBS electrostatic potential values in various points on the surface? Is there such feature already in Chimerax that I missed? Such feature is essential (I think) to monitor subtle changes in surface potential following mutations or other variations (pH, salt concentration etc.). If it's not there yet, could you please add it to the (enormous, I guess) to-do list? In Chimera this is done by moving the cursor to the various points of interest, a feature that I found most useful (and helpful in convincing color blind referees 😉). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

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Re: [chimerax-users] Problems with Measuring Angles in ChimeraX
by Elaine Meng 10 Sep '21

10 Sep '21

> On Sep 10, 2021, at 11:41 AM, liangb2 <liangb2(a)rpi.edu> wrote: > > Hi Elaine: > I'm new to ChimeraX for Cryo-EM data. Currently, I imported my tomogram (.mrc file) into ChimeraX and acquired a density map of it. I was able to get the x,y,z coordinates of the three points of interest. However, I was not able to find ways to measure the angle among the three points on the tomogram density map. I have looked up tutorials, but all of those I have found are for proteins. > > Can you please provide some help on how I can measure the angle among three points on the density map? I would really appreciate your help. > Thank you for your time! > Best, > Biqing Liang Hi Biqing, Welcome to ChimeraX! We recommend using the chimerax-users(a)cgl.ucsf.edu address for asking questions (CC'd here so you don't need to do anything). Depending on the question, other people might want to see the answer, or give better answers than mine, or I might not know the answer at all. I don't know how you got the X,Y,Z coordinates for those three points. The way I know how to do it: You can put several "markers" (balls, fake atoms) at points on the surface, and/or at peaks in the density values. Then you can select any 3 of the markers (Shift-Ctrl-click on them) and then use the "angle" command: angle sel <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html> The way to put markers on interactively is first to go to the Markers toolbar across the top of the ChimeraX window. The different icons assign different ways of adding markers by mouse click. For example, clicking the third from left icon in the Markers toolbar assigns the right mouse button (= trackpad + Alt on Windows, trackpad + command key on Mac) to adding markers on the surface. See the following for what the different icons mean and explanation of markers: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markers.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Question.
by Yunsik Kang 10 Sep '21

10 Sep '21

Hello, My name is Yunsik Kang, and I am a postdoc in Marc Freeman's lab at the Vollum Institute. I would love to use ChimeraX to predict the structure of my protein of interest. I watched all the YouTube videos and tried to run the program. Unfortunately, my protein is 5005 amino acids in humans and 2958 aa in yeast. I get a message "Please use the full AlphaFold system for long sequences." My question is what is the best way to approach this problem? Should I cut the protein in half and run the program? In one of the videos, it mentions after 700 aa it will have problems. Will it work if I get Colab-Pro? Or would the server crash no matter what. I am not a structural biologist, but I hope the structure can help be predict me with my research. Thank you, Yunsik

4 7

Help with Volume Series
by Ioannis Skalidis 10 Sep '21

10 Sep '21

Greetings to all! I am trying to play a volume series data in ChimeraX (daily build). I open the multiple .mrc frames and they are automatically grouped, but then, when I use the vseries play command, I get an error message that I have not specified a volume series. What am I doing wrong? Should I open the frames differently? I also tried to open them with the open command, a wildcard character for the frame names and vseries true modifier but even then, it only opens the first frame, which I found very strange as well. Could somebody offer some advice? It would be greatly appreciated! Cheers, Yiannis. -- Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/

2 1

Re: [chimerax-users] [ChimeraX] #5198: Transparent background not transparent when selection outline shown
by Zhao, Bingchun (NIH/VRC) [F] 10 Sep '21

10 Sep '21

Hi, Tom, I received this below email reported that this bug has been fixed. Do I need to download the latest version and re-install the ChimeraX? Thank you very much! Best, Bingchun On 9/9/21, 9:35 PM, "ChimeraX" <ChimeraX-bugs-admin(a)cgl.ucsf.edu> wrote: #5198: Transparent background not transparent when selection outline shown --------------------------------------+------------------------- Reporter: bingchun.zhao@… | Owner: Tom Goddard Type: defect | Status: closed Priority: normal | Milestone: Component: Graphics | Version: Resolution: fixed | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | --------------------------------------+------------------------- Changes (by Tom Goddard): * status: assigned => closed * resolution: => fixed Comment: Fixed. Offscreen rendering was making a framebuffer with no alpha channel, even though for image save it already had an offscreen framebuffer with alpha channel. Made offscreen check and not create a new framebuffer if we are already using an offscreen framebuffer. -- Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5198#comment:3> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> ChimeraX Issue Tracker

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outline the interface region in chimeraX
by Zhao, Bingchun (NIH/VRC) [F] 09 Sep '21

09 Sep '21

Hi, I wonder if there is a way to outline the interface region in ChimeraX like below: [cid:image001.png@01D7A597.5344EDF0] Previously, I did this in photoshop, but can we label the interface regions with those lines in ChimeraX? Thank you very much! Bingchun Bingchun Zhao, PhD Postdoctoral, VF Biodefense Research Section VRC/NIAID/NIH Bldg 40, Room 2607B 40 Convent Drive Bethesda, MD 20892 Tel: 301-761-7649 Email: bingchun.zhao(a)nih.gov<mailto:bingchun.zhao@nih.gov>

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Re: [chimerax-users] getting AlphaFold predictions
by Elaine Meng 09 Sep '21

09 Sep '21

Hi Yk, Forwarding to chimerax-users(a)cgl.ucsf.edu since I don't have a good answer for this currently. (We prefer you use that address for questions unless they include some data that needs to stay private.) Thanks! Elaine > On Sep 9, 2021, at 1:57 PM, Yunsik Kang <kangy(a)ohsu.edu> wrote: > > > Hi Elaine, > > Thank you again! > > I did open it and using ChimeraX I can see the pdb files and see the structure! It is amazing! > > One question. > > Since my protein is massive and this is just parts of my protein, is there a way ChimeraX can stitch it all together? > > Like Tristan says it is 1400 residues each, can I perhaps somehow stitch the whole thing together? > > Yk > > -----Original Message----- > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Thursday, September 9, 2021 8:12 AM > To: Yunsik Kang <kangy(a)ohsu.edu> > Cc: meng Elaine <meng(a)cgl.ucsf.edu> > Subject: [EXTERNAL] Re: [chimerax-users] getting AlphaFold predictions > > Hi Yunsik, > I do not know the answer to your questions. We are not the developers of AlphaFold or the AlphaFold database. We only added tools in ChimeraX to connect to them. > > Maybe there is information at the AlphaFold database about what's in their download. I have never downloaded these myself. > <https://www.alphafold.ebi.ac.uk/download> > > All I know is that "tar" is a way of putting multiple files together and that you have to "untar" to get them apart. This is a standard computer file thing, not related to any specific kind of files. > > Usually if you doubleclick the tar file your computer will automatically untar it and make some new folder or folders containing the files. You would need to have enough space available on your computer for the large number of files. > > I don't know how they are named but maybe there is a README file that comes with it, or if not, you may need to look at the files with a text editor. Maybe they have the Uniprot IDs of the proteins somewhere in the names or header text of the file. > > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On Sep 8, 2021, at 7:36 PM, Yunsik Kang <kangy(a)ohsu.edu> wrote: >> >> Hi Elaine, >> >> Thank you for the fast response. My proteins are not found in the Alphafold search. >> >> I am new to this so bear with me. I downloaded the human TAR file as Tristan has said, but have no idea how to search or even start looking for my protein. >> >> Could you help? Or is this something I need professional help with? >> >> Would it help to tell you the protein I am interested in? >> >> Thank you again. >> Yunsik >> >> From: Elaine Meng <meng(a)cgl.ucsf.edu> >> Sent: Wednesday, September 8, 2021 3:44 PM >> To: Yunsik Kang <kangy(a)ohsu.edu> >> Subject: [EXTERNAL] Fwd: [chimerax-users] getting AlphaFold >> predictions >> >> Forwarding in case you did not get Tristan's reply below: >> >> >> Begin forwarded message: >> >> From: Tristan Croll via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> >> Subject: Re: [chimerax-users] getting AlphaFold predictions >> Date: September 8, 2021 at 3:17:28 PM PDT >> To: ChimeraX Users Help <ChimeraX-users(a)cgl.ucsf.edu> >> Reply-To: Tristan Croll <tic20(a)cam.ac.uk> >> >> The human protein will be in the EBI-Alphafold2 database, but not accessible to the search tool. For human proteins (and only human, so far) longer than ~2000 residues, the predictions are provided as multiple 1400-residue fragments starting at residue 1, 201, etc.. The only way to get those right now is to download the tarball of the complete set of human protein predictions, and find them in there. >> >> >> On 8 Sep 2021, at 23:08, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hi Yunsik, >> I don't know where/how you can run a prediction for such a long sequence, maybe others can comment on that. However: >> >> First make sure there is not already a predicted structure for that protein in the AlphaFold Database! E.g. try the Search button on the AlphaFold tool and see if the same UniProt entries as you are interested in are found. The database includes human and other well-studied species (maybe also the yeast you mentioned, depending on the exact species). If the prediction is already in the database, there is no need to run a new calculation. >> >> ChimeraX AlphaFold tool: >> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry University of California, San >> Francisco >> >> >> On Sep 8, 2021, at 2:45 PM, Yunsik Kang via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hello, >> >> My name is Yunsik Kang, and I am a postdoc in Marc Freeman’s lab at the Vollum Institute. >> >> I would love to use ChimeraX to predict the structure of my protein of interest. I watched all the YouTube videos and tried to run the program. >> >> Unfortunately, my protein is 5005 amino acids in humans and 2958 aa in yeast. I get a message “Please use the full AlphaFold system for long sequences.” >> >> My question is what is the best way to approach this problem? Should I cut the protein in half and run the program? In one of the videos, it mentions after 700 aa it will have problems. Will it work if I get Colab-Pro? Or would the server crash no matter what. >> >> I am not a structural biologist, but I hope the structure can help be predict me with my research. >> >> Thank you, >> Yunsik >> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> > >

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Save pdb file
by Zhao, Bingchun (NIH/VRC) [F] 09 Sep '21

09 Sep '21

Hi, First, I wanna thank you for all your work to develop ChimeraX, it’s so powerful. I do have a question and would like to have your input. I opened a EM density map (.mrc) and two pdb files in chimerax (version 1.2), then fit all the pdb models into the EM map. Then, I hide the EM map, only show the pdb models after fitting, and then I would like to save these all pdb files in a new pdb file with all position information after fitting. Would you please give me any direction how to do this? I tried saving them, but only partial pdb files saved, also tried combine commend, but it said no such commend. Thank you very much! Best, bingchun Bingchun Zhao, PhD Postdoctoral, VF Biodefense Research Section VRC/NIAID/NIH Bldg 40, Room 2607B 40 Convent Drive Bethesda, MD 20892 Tel: 301-761-7649 Email: bingchun.zhao(a)nih.gov<mailto:bingchun.zhao@nih.gov>

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error saving a surface
by Diego Amaya 08 Sep '21

08 Sep '21

Hi, I'm running a python script in --nogui and --script mode and I'm getting an error when doing rc(session, 'save surface.stl format stl'). The error message is : *QGuiApplication::font(): no QGuiApplication instance and no application font set.Segmentation fault* I'm working with debian 10 and I used the production release 1.2.5-1 Thanks in advance for the help. -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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capture reply from run(session, command)
by Sean Connell 08 Sep '21

08 Sep '21

Hello I was wondering if it is possible to capture the output that goes to the log when you run the python command run(session, command). For example if I run: run(session, "mmaker #2/A to #1/A”) Can I store in a variable the reply in the log file that has information about the RSMD? Sean

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distance between centers of mass using python API
by Diego Amaya 08 Sep '21

08 Sep '21

Hello, I'm trying to compute the distance between the centers of mass of two residues using the python API. I tried two different ways : 1. *rc(session, 'define centroid :43 massWeighting true name AA1')rc(session, 'define centroid :35 massWeighting true name AA2')rc(session, 'distance AA1 AA2') * 2. *rc(session, ' measure center :43 mark true name AA1')rc(session, 'measure center :35 mark true name AA2')rc(session, 'distance AA1 AA2')* But I get this error in the third line in both cases : *chimerax.core.errors.UserError: Missing or invalid "objects" argument: invalid objects specifier * What is wrong ? Thanks in advance. -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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Question about use of ChimeraX
by Jonathan Choong 07 Sep '21

07 Sep '21

Hi there, Hope you are doing well. I just had a question regarding ChimeraX that I was hoping to get some clarity on. I was wondering whether it was possible to use ChimeraX commands (such as open, run, save) in the system command line without actually opening the application interface? Thanks, hope to hear back from you. Kind regards, Jonathan

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Re: [chimerax-users] [Chimera-users] matchmaker for more than one chain
by Elaine Meng 03 Sep '21

03 Sep '21

Hi Mani, There is a different e-mail address for ChimeraX questions: it is chimerax-users(a)cgl.ucsf.edu CC'd here. Responses below... > On Sep 2, 2021, at 2:22 AM, manikandank via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi ChimeraX-users, > I have used recently the mmaker cmd to align two pdb each have multiple chains as below. > > mmaker #12/L,M,N to #5/S,A,B matrix blosum-62 showAlignment true > > But the sequence view shows only the alignment of chain L and S. > > 1. I would like to have aligned sequences of all chains used in mmaker alignement. Your command above does not use all the chains for fitting, it only chooses the single pair of chains that gives the best sequence-alignment score to superimpose the two models. The other chains might look superimposed but it is only because they moved along with the ones that were actually used for the fit. To use all three pairs of chains, you need to also use the "pairing ss" option: mmaker #12/L,M,N to #5/S,A,B matrix blosum-62 showAlignment true pair ss Then you would get three pairwise sequence-alignment windows: L/S, M/A, and N/B. matchmaker or mmaker command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> pairing options <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> > > 2. Is it possible to open the saved RMSD header values in a file later just to color the pdb? Yes, but with several steps so it may not be that convenient. Probably easier just to save and restore the ChimeraX session (which includes the sequence alignment windows). Also remember if you move the structures relative to each other, the RMSD values will change. However, if you really want to save the RMSD values to file after you showed sequence alignments and header, then you could save them as an attribute file (that could be reopened/applied later): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> The attribute name is seq_rmsd as explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers> > > 3. Do mmaker align entire pdb based on selected chains and Can calculate RMSD for all residues in the pdb? For the first question, 3A: yes, depending on the "pairing" option as explained above. For the second question, 3B, I'm not sure what you want. Remember that the main purpose of matchmaker is to superimpose the structures well, and then it happens to also give the RMSD over the positions that it chose to use, which are shown in the pinkish boxes on the sequence alignment. By default it uses fit iteration and discards loops that don't superimpose well in space. Matchmaker only gives the RMSD over the positions it uses. You could tell it to use all positions, but that would change the superposition. If you like the default superposition (that does not use all of the positions), you can use a separate command "rmsd" to measure RMSD over any sets of atoms that you want, without moving the structures or changing the superposition. Or, if you really want to use all of the positions in the sequence alignment for the fitting, you would have to use matchmaker option "cutoff none" ... but that usually does not give the best superposition. cutoff option <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#cutoffDis…> rmsd command (calculate RMSD in current positions, no fitting) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html> Matchmaker only gives alpha-carbon RMSD. The rmsd command can give RMSD for any sets of atoms that you want, alpha-carbons only, or backbone only, or all atoms, as long as you give equal numbers of atoms from the two structures. However, it can be tricky to specify the correct sets of atoms if the residue numbering or residue types are different between the two structures. So you might want to first use "mmaker" with whichever options give you the best superposition, and then to measure RMSD over all positions in the alignment (which might not be used in the matchmaker fit), use the "rmsd" command afterward. > > 4. I also would like to change the displayed text for the sequence name. Presently it puts the filename as sequence name. > > [similar to 'Edit sequence name' in the sequence viewer in chimera] Sorry, there is no way yet to change the displayed sequence name in ChimeraX. > > Please let me know how this can be done. > thank you very much > with kind regards > Mani. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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bundle dependency not installed
by Lagerwaard, I.M. (Ilse) 02 Sep '21

02 Sep '21

Hello, I'm currently developing a bundle with a dependency on pandas. Even though I included this dependency in my bundle_info.xml file, I get "ModuleNotFoundError: No module named 'pandas'". For now, I have installed pandas on the ChimeraX console via the command prompt. For future distribution, however, it would be nice if it were immediately installed together with the bundle. I would greatly appreciate your help with this issue. Thanks in advance, Ilse

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Re: [chimerax-users] output mmCIF file
by Elaine Meng 02 Sep '21

02 Sep '21

> On Aug 31, 2021, at 1:50 PM, Liu, Xiangan <Xiangan.Liu(a)uth.tmc.edu> wrote: > > Hi, > I have issue to output the models I build in pdb formation to mmCIF formation. I did not provide the sequences in orginal pdb files. Could please let me know what is the problem and how to fix it? > Thanks, > Xiangan > ---------- > File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/mmcif/__init__.py", line 89, in save > mmcif_write.write_mmcif(session, path, **kw) > File "src/mmcif_write.pyx", line 145, in chimerax.mmcif.mmcif_write.write_mmcif > File "src/mmcif_write.pyx", line 149, in chimerax.mmcif.mmcif_write.write_mmcif > File "src/mmcif_write.pyx", line 542, in chimerax.mmcif.mmcif_write.save_structure > KeyError: ('a1', 'RPGMMDSQEFS') > > KeyError: ('a1', 'RPGMMDSQEFS') > > File "src/mmcif_write.pyx", line 542, in chimerax.mmcif.mmcif_write.save_structure Hi Xiangan, We recommend using the chimerax-users(a)cgl.ucsf.edu address for questions (CC'd on this message, so you don't need to do anything this time). The address you used is just for commercial licensing. Actually, if you get a traceback like this, you can usually use ChimeraX menu: Help... Report a Bug instead of sending e-mail. You may need to attach your session file so that we can reproduce the problem. I don't know the answer, so I'm using this address to share your question with the others. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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ChineraX saves huge session files
by Dror Noy 31 Aug '21

31 Aug '21

Hi Recently, ChimeraX on my Mac (macOS Catalina) started saving very large session file. Regardless of the size of the pdb file I load - the session file is 124 MB even for small 2-3 MB pdb files. I’d appreciate any help. Thanks Dror

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Region-wise specific sub-coloring of SS elements
by Gupta, Arun 30 Aug '21

30 Aug '21

Dear ChimeraX team, Is there an easier way around by which we can do region-wise specific sub-coloring of secondary structural elements within a large protein instead of using the tedious way of identifying the secondary structural elements and then describing the residue wise specific selection of set of residues related to secondary structure elements? I am aware that we can do coloring of specific secondary structure elements in ChimeraX by following commands for e.g “color helix “darkcyan” targ c”. But, I am looking forward to do coloring, let’ say “all the helices within a protein from residues 1-300 as dark cyan and residues 300-500 as blue” Thanks!!! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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