- ChimeraX-users - RBVI Mailing Lists

Ask for help with chimeraX
by 泡沫 24 Feb '22

24 Feb '22

     We love the software you developed, ChimeraX. With high-performance rendering of large structures and data, the ability to quickly and microfiber slim readers and write millimeter ciliates, fast and robust solvent elimination surfaces, interactive ambient occlusion lighting, and curved cylindrical "tube" spirals with cartoon integration, our research team especially loves your software. Compared with UCSF Chimera1.16, we found that ChimeraX lacks the function of Organization, but we really need this function, how can we choose to use ChimeraX to solve the problem of missing this function? Can we use this feature as an external software plug into The ChimeraX?       Hope to get help from your school and restore me, thank you.

1 0

Re: [chimerax-users] alphafold predict stops after MSA step (google colab pro)
by Rangarajan, Amith 23 Feb '22

23 Feb '22

Hi, I am new to using alphafold for prediction, i tried today with a reasonable size model ( 400 AA ) of a kinase domain. i opted to use 'high RAM " available on colab pro and after running for an few hours , the job stops without any error, the colab notebook had disconnected due to inactivity and it did not generate any models. please share with me your experience of using alphafold from within chimerax , helpful tips to get the job to finish . here is the output ( output on google colab): Sequence length 401 Have Colab GPU runtime Installing HMMER for computing sequence alignments Installing matplotlib to plot sequence alignment coverage Installing AlphaFold Installing OpenMM for structure energy minimization Finding fastest mirror for sequence databases using united states Searching sequence databases (147 Gbytes). Search will take 29 minutes or more. Searching uniref90 sequence database, 59 Gbytes 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 Searching smallbfd sequence database, 17 Gbytes 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Searching mgnify sequence database, 71 Gbytes 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 Computing multiple sequence alignment 327620 similar sequences found (311112 uniref90, 16008 smallbfd, 500 mgnify) [cid:4e178c51-cd4c-4958-b2e8-fa714cbfcd07] Computing structures using 5 AlphaFold parameter sets: model_1 thanks a lot again for all your support, best amith

2 1

Drawing objects in ChimeraX?
by de Miranda Seabra, Gustavo 23 Feb '22

23 Feb '22

Hi, I was wondering if it is possible to draw objects in ChimeraX. More specifically, I'd like to show the gridbox used for docking calculations, so it would be nice if I could draw a cube, and even better if it can be drawn as a surface that could have color, transparency, etc. How to do this in ChimeraX? Thanks a lot! -- Gustavo Seabra Research Associate Professor Center for Natural Products, Drug Discovery, and Development (CNPD3) Department of Medicinal Chemistry College of Pharmacy University of Florida, Gainesville, FL, USA

3 4

Re: [chimerax-users] Regarding generating volume surface in ChimeraX for large maps
by Tom Goddard 22 Feb '22

22 Feb '22

Hi Rakesh, ChimeraX displays just a single plane when you open a map file larger than 256 Mvoxels -- often the situation for electron microscopy tomograms, for example a 2048 by 2048 by 100 map (400 Mvoxels), but also for large electron microscopy single particle reconstructions, e.g. 800 x 800 x 800 (512 Mvoxels). Maps larger than 16 Mvoxels will not be shown at full resolution (step 1), instead the step size will be chosen to only display at most 16 Mvoxels when the map is first opened, again to improve load speed for common interactive use cases. So if you are writing a script and need the full map shown always include a volume command to assure it is shown how you want, for example to show all planes, volume #1 region all style surface or to assure it is shown at full resolution volume #1 step 1 region all style surface and to make sure the threshold level is what you want you can specify it too volume #1 level 4.5 step 1 region all style surface There are volume command options that set the 256 MVoxel limit for planes (option name "voxelLimitForPlane") and 16 MVoxel full resolution limit (option name "voxelLimit") that you can use to change the default for the current session, but unfortunately ChimeraX currently does not offer a way to save new default values. These are all documented https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling Tom > On Feb 18, 2022, at 12:47 PM, Rakesh Ramachandran <rakeshramachandran10(a)gmail.com> wrote: > > Hi Tom, > > I am trying to segment volume using 'volume splitbyzone' in ChimeraX for a large number of maps. But what I observed is that some of the maps are displayed as planes instead of surfaces and this affects the volume splitbyzone command. > > I tried using 'volume style surface' but it doesn't seem to work unless I manually set it in the GUI. What option do I use to generate surfaces for map volumes automatically from the command line in such cases? > > -- > Regards > Rakesh Ramachandran > Postdoctoral Scholar > Department of Bioengineering and Therapeutic Sciences > University of California, San Francisco > Byers Hall Room 501 > 1700 4th Street > San Francisco, CA 94143, USA

2 2

Editing preset for initial colors
by Niels Bradshaw 22 Feb '22

22 Feb '22

Hi Elaine, Is there a way in chimera X to change the initial colors preset for new models? I’m not into the default tan color, so I end up changing the color immediately every time I open a new model. In previous versions of Chimera, I had disabled color by model and set all new models to open with grey. In pymol, I defined the colors for the first 10 models I open in the startup script, which is even more convenient. Having the option to have the default to color by chain could also be nice if that is possible. I tried some workarounds like redefining the tan color, but it appears that is not allowed. Thanks, Niels

4 3

Re: [chimerax-users] Mailman privacy alert
by Ralph Loring 22 Feb '22

22 Feb '22

Hi, I keep getting these notifications that ChimeraX on both my laptop and my office computer is not registered and I need to register them again. I think between the two computers, I've registered the program four times in the past two months. What's up with this? Ralph Loring 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 On Thu, Feb 17, 2022 at 8:32 PM <chimerax-users-bounces(a)cgl.ucsf.edu> wrote: > An attempt was made to subscribe your address to the mailing list > chimerax-users(a)cgl.ucsf.edu. You are already subscribed to this mailing > list. > > Note that the list membership is not public, so it is possible that a bad > person was trying to probe the list for its membership. This would be a > privacy violation if we let them do this, but we didn't. > > If you submitted the subscription request and forgot that you were already > subscribed to the list, then you can ignore this message. If you suspect > that > an attempt is being made to covertly discover whether you are a member of > this > list, and you are worried about your privacy, then feel free to send a > message > to the list administrator at chimerax-users-owner(a)cgl.ucsf.edu. >

2 1

Re: [chimerax-users] Bundle dependency
by Anthony James Schaefer 21 Feb '22

21 Feb '22

Katie, I'm not sure. I tried adding pdb-objects to one of my bundle's dependencies, and it was installed. I'm testing this on a ChimeraX 1.4 daily build. My bundle_info.xml has this: <Dependencies> <Dependency name="ChimeraX-Core" version=">=1.2.dev"/> <Dependency name="pdb-objects"/> </Dependencies> and my log has this after installing (along with a bunch of other stuff): Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\normn\documents\github\chimerax_themes\dist\chimerax_themes-0.3.1-py3-none-any.whl Requirement already satisfied: ChimeraX-Core>=1.2.dev in e:\chimerax 1.4.dev202202010639\bin\lib\site-packages (from ChimeraX-themes==0.3.1) (1.4.dev202202010639) Collecting pdb-objects Using cached pdb_objects-0.1.3-py3-none-any.whl (6.6 kB) Installing collected packages: pdb-objects, ChimeraX-themes Successfully installed ChimeraX-themes-0.3.1 pdb-objects-0.1.3 --- Successfully installed ChimeraX-themes-0.3.1 pdb-objects-0.1.3 Installed ChimeraX-themes (0.3.1) Towards the bottom, it says it installed pdb-objects and my bundle. I can then go into the shell and import pdb_objects without error. Best, Tony ________________________________ From: Zeng, Katie <jingrou.zeng18(a)imperial.ac.uk> Sent: Monday, February 21, 2022 2:59 PM To: Anthony James Schaefer <tony.schaefer(a)uga.edu> Subject: Re: Bundle dependency [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi Tony, Thanks for pointing that out. I've now changed the dependency to pdb-objects, but I still get the same error when I try to use the bundle in ChimeraX. Have you got any idea why it's giving this error? Best Regards, Katie ________________________________ From: Anthony James Schaefer <tony.schaefer(a)uga.edu> Sent: 21 February 2022 17:57 To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu>; Zeng, Katie <jingrou.zeng18(a)imperial.ac.uk> Subject: Re: Bundle dependency This email from tony.schaefer(a)uga.edu originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. Katie, It looks like PDB objects on PyPI is called pdb-objects, not pdb_objects. For dependencies, ChimeraX looks for the package name and not the import name. Best, Tony ________________________________ From: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu> on behalf of Zeng, Katie via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Sent: Monday, February 21, 2022 11:50 AM To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] Bundle dependency [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi, I'm currently working on building a membrane builder bundle and it requires the use of a python library called 'pdb_objects'. Following the tutorial on the website, I'm adding the following line to my bundle_info.xml file under the dependencies tag: <Dependency name="pdb_objects"/> It still gives me an error of <No module named 'pdb_objects'> when I load my bundle in ChimeraX. How can I allow the use of this library in my bundle? Thanks for your help! Best Regards, Katie

1 0

Bundle dependency
by Zeng, Katie 21 Feb '22

21 Feb '22

Hi, I'm currently working on building a membrane builder bundle and it requires the use of a python library called 'pdb_objects'. Following the tutorial on the website, I'm adding the following line to my bundle_info.xml file under the dependencies tag: <Dependency name="pdb_objects"/> It still gives me an error of <No module named 'pdb_objects'> when I load my bundle in ChimeraX. How can I allow the use of this library in my bundle? Thanks for your help! Best Regards, Katie

2 1

Re: [chimerax-users] No suitable models found for viewDockX
by Rangarajan, Amith 21 Feb '22

21 Feb '22

hello chimeraX, I am trying to open a glide docking result using viewdockx and i am getting this error message ('no suitable models found"). I tried opening the file as .mae file ( protein and ligand are both in same model )and a pv.mae file ( protein and ligand are in diff models). I am still getting the same error. I am using chimerax ver 1.3 please help me see what i am missing. thanks amith

2 1

Question about Coulombic electrostatic potential
by Sunisa Yoodee 21 Feb '22

21 Feb '22

Dear UCSF ChimeraX We used the ChimeraX program to calculate electrostatic potential. By using the coulombic command, a molecular surface was generated and colored. However, we also need the electrostatic potential value (kcal/(mol*e))of the protein. Could you please give some advices how to get this value? Best Regards, Sunisa Yoodee -- *Sunisa Yoodee*, Ph.D Medical Proteomics Unit, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, THAILAND Tel: 66-8-06691102 e-mail: yd.sunisa(a)gmail.com

3 3

Define axis tool missing?
by James Hodgkinson-Bean 20 Feb '22

20 Feb '22

Hi I am currently doing some geometric analysis of a protein complex, and was wanting to define certain axis normal to planes I have defined; on the online chimerax documentation there seems to be an option “define axis”, however in my actual chimeraX program, this command doesn’t work, and is not listed under the “help define” command which shows how to define planes and centroids. I am running ChimeraX version 1.3 (2021-12-08), which I downloaded recently. Any assistant would be much appreciated 😊 P.S I absolutely love chimeraX!! It is one of the best pieces of software I’ve ever used. Cheers, James.

2 1

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

3 10

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

3 2

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

2 2

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/

2 2

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)

3 4

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

1 0

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

3 3

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>

2 1

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

2 1

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

2 1

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

2 1

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

2 1

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/

2 3

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

2 2