- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] trouble with importing chimerax module
by Tom Goddard 05 Mar '21

05 Mar '21

Hi Greg, ChimeraX like Chimera includes Python within the application. So the normal way to run a ChimeraX Python script is to just open it in ChimeraX for example with the open command "open myscript.py" or you can run ChimeraX from a shell without a graphical user interface and have it run the script chimerax --nogui myscript.py With Chimera there is a pychimera PyPi module (https://pypi.org/project/pychimera/ <https://pypi.org/project/pychimera/>) created by Jaime Rodriguez-Guerra outside our lab to use Chimera with your own Python 2 installation. There currently is not a PyPi module to use ChimeraX in your own Python 3. I made a ChimeraX PyPi module (a "wheel") a few months ago as a test but it only partly works and we have not released it. Various initializations in the ChimeraX code need to be fixed to work outside the ChimeraX application. We proposed doing that work in a grant application to Chan-Zuckerberg Initiative last month, their Visual Proteomics call for proposals (https://chanzuckerberg.com/rfa/visual-proteomics/ <https://chanzuckerberg.com/rfa/visual-proteomics/>). We will not know whether we get funding to pursue that until at least May 2021. Is it essential to your use of ChimeraX that you run Python scripts in your own Python? If so we could try to get something rigged up that would work for you. If the main issue is you need other PyPi packages that are not in ChimeraX for your Python scripts, you can install those packages easily into ChimeraX using chimerax -m pip install <NameOfPyPiPackage> Tom > >> On Mar 5, 2021, at 12:49 PM, Gregory Babbitt <gabsbi(a)rit.edu> wrote: >> >> Hi Dr. Meng >> >> Some of us at RIT are having trouble importing chimerax.core.commands to python3 so we can write a script to run things in chimerax. >> >> Does debian have it? I also noticed my pip list does not show the older chimera module even though we call it alot in python. Does it have a different name like midas or pychimera? >> >> What is chimeraX equivalent...how do we install it via pip/pip3? >> >> thx >> >> Greg B >> >> Dr. Gregory A Babbitt >> Associate Professor >> T.H. Gosnell School of Life Sciences >> Rochester Institute of Technology >> Rochester NY USA >> website: http://people.rit.edu/gabsbi >> >> > >

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chimera X troubles
by Dorian Armando Acevedo Castro 05 Mar '21

05 Mar '21

Good morning, I tried to install chimera X for Ubuntu 16 but I have the following problem. (base) da.acevedo10@colab14:~$ sudo apt-get install /home/UANDES/da.acevedo10/chimerax-daily.deb Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'ucsf-chimerax-daily' instead of '/home/UANDES/da.acevedo10/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: ucsf-chimerax-daily : Depends: ffmpeg but it is not installable E: Unable to correct problems, you have held broken packages. I really appreciate if you can tell me why I can't install chimera x Cordialmente, Dorian Armando Acevedo Castro COBO - Computational Bio- Organic Chemistry Bogotá cobo.uniandes.edu.co<http://cobo.uniandes.edu.co/> Estudiante Doctorado Ciencias-Química. M. Sc. Química, U. de los Andes. Químico, U. Nacional. <mailto:daacevedoc@bt.unal.edu.co> <mailto:dorian.acevedo@gmail.com>

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An urgent question about Chimera (need help)
by 陆萌 05 Mar '21

05 Mar '21

Dear developers: I have always failed to minimize my structure in Chimera, even if I reinstalled my Chimera or tried another version of Chimera. I can not fix this bug by myself, so I have to ask for help to you. I'll appreciate very much if you can help me solve the problem. Thank you very much! Sincerely! Meng Lu 2021.3.5

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Attribute files in ChimeraX
by David Leeming 04 Mar '21

04 Mar '21

Dear ChimeraX users, I'm trying to write a script that will export an attribute file in ChimeraX, (specifically the attribute sasa) I'm looking for a similar output to that of the attribute calculator function in Chimera (see image below) [cid:9fd01eec-1765-4ec9-8172-dec4315fa1d6] I'm currently trying to run the command below to export the attribute file: [cid:6e286ca4-a133-49bc-a34e-1a2f39bb7243] However, when I run this script, it produces the error: "No known data format for file suffix '.defattr'" Any advice on how I can better go about producing this file or how I can modify my script to prevent this error would be greatly appreciated. Thank you for your time. Kind regards, David

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Re: [chimerax-users] How to expand the RAN in ChimeraX?
by Tom Goddard 03 Mar '21

03 Mar '21

Hi Andrea, The volume command dataCacheSize option will do this. For example for 32 Gbytes of memory cache for volume data use command volume dataCacheSize 32000 The default is to set it to half the physical memory of the computer. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling> I would not suggest changing it because surface and image rendering typically use an amount memory for the graphics similar to the data size. The cache is only for the volume data, so with graphics, the current setting can utilize all your memory. Increasing it can cause data to be paged out to disk with horrible performance. The above setting is not saved. If you did want to change it for every ChimeraX session you would use Preferences / Startup / Execute these commands at startup. Tom > On Mar 3, 2021, at 9:04 AM, Andrea Fera <andrea.fera(a)revealgc.com> wrote: > > Dear Mr. Goddard, > > This is Andrea. I am not sure that you remember me, but we met in 2013 or so in S. Francisco and Berkeley. > > I am a strenuous fan of your software! Especially for volume rendering of cryo-type tomograms. > I do have a tomogram pf a few Gb that I would like to render with your software. I use a Lynux server with LOTS of RAM. How can I increase the RAM allocated by ChimeraX? > > Thank you and all best… > Andrea Fera > > -- > Andrea Fera, PhD > Senior Data Scientist > <image003.jpg>

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Accessing shapes created through a .BLD script
by Tanmoy Sanyal 03 Mar '21

03 Mar '21

Hi, I have a bunch of shapes (spheres and cylinders) created through a .bld script. I'd like to load this script once, and then be able to change the colors of said shapes in successive operations. It is possible to set the colors directly in the .bld script, but I need to make an animation out of this. E.g: if my .bld script contains lines that draws shapes like so: .sphere 0 0 -1 5.0 .cylinder 0 0 0 1 1 1 1.0 I want to be able to later have a bunch of scripts called 1.cxc, 2.cxc, 3.cxc, .... each of which change the color of the sphere and cylinder. This way, I can load these scripts in the per-frame mode, to create an animation out of the color changes. Alternatively, I tried doing this with just the shape command and without a .bld script, but I have over ~10000 shapes; the shape command interprets each as a different model, and my computer hangs. ----- Thanks, Tanmoy Tanmoy Sanyal Postdoctoral scholar, Sali lab <https://salilab.org/>, Department of Bioengineering and Therapeutic Sciences <https://bts.ucsf.edu/>, University of California San Francisco Phone:- (+1) 805-637-0375

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Help with surfaces
by Eoin Winston 02 Mar '21

02 Mar '21

Hello, I create molecular animations and use ChimeraX to import PDB files and convert them to surfaces which I then export for use in Autodesk 3dsmax. I have a very limited understanding of this fantastic software however I am wondering if there is a quick way to solve my problem. I have a PDB file I was sent containing a trimer. When I use a command such as: *molmap #13,1 20 *(I found this on a YouTube video BTW) It creates a surface model of the entire PDB file. How do I create separate surface models for each of the trimers? So the PDB exports with three meshes as opposed to a single mesh. Hope that makes sense. Best regards, Eoin *Eoin Winston, *Head of Design *Phone:* +353 877991603 | Email <eoin(a)nexucreative.com> | Web <http://www.nexucreative.com/> | Instagram <https://www.instagram.com/NEXU.creative/> | Twitter <https://twitter.com/NEXU_Science> Raptech Ltd. t/a *NEXU* Science Communication is registered in Ireland as a private company limited by shares. Registration No. 610585. Registered business address: 3 Mruigtuaithe, Ratoath, County Meath, Ireland. A85 Y883

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Re: [chimerax-users] [Chimera-users] calculating % exposed surface area
by Tom Goddard 25 Feb '21

25 Feb '21

Hi Elaine, Good point. Forgot ChimeraX computes SAS area and not SES area. It makes more sense from a science perspective to use SAS I think -- the functionally relevant quantity is how much room there is for a ligand to be in contact and I think SAS will better reflect that than SES, although the correlation is no doubt very high between SES and SAS areas. Tom > On Feb 25, 2021, at 10:40 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Currently it is not possible to use ChimeraX for this specific workflow, however, because it does not calculate residue solvent-excluded surface (SES) area values. The values supplied for normalization in that page (to calculate % exposed) are SES calculated with the Chimera parameters. These were kindly supplied by another group, as cited in that page. > <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html > > > The ChimeraX command "measure sasa" measures solvent-accessible surface (SAS) area and can assign the per-residue and per-atom values as attributes. > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> > > Theoretically somebody could generate the GXG tripeptides as proxy for the fully exposed state and measure SAS for each X in ChimeraX to compile a list of suitable values for normalization to calculate % exposed, but as far as I know, it hasn't been done. > > Here's diagram showing the difference between SES and SAS for those who may not be familiar with these terms: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#surfdefs> > > Elaine > > >> On Feb 25, 2021, at 9:54 AM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi David, >> >> Maybe your structure has ligands, ions, or solvent atoms -- no surface is computed for those and so they don't get an areaSES attribute. You could put in a check >> >> if hasattr(r, 'areaSES'): >> r.relSESA = r.areaSES/ r.areaSESgxg >> else: >> print 'Residue has no areaSES', r, 'type', r.type >> >> You might be interested instead using our newer program ChimeraX. Chimera often fails to compute molecular surfaces and SES areas for large structures. ChimeraX uses new code that always works. >> >> Tom >> >> >>> On Feb 25, 2021, at 5:53 AM, David Leeming <david.leeming(a)student.manchester.ac.uk> wrote: >>> >>> Dear Chimera users, >>> I'm attempting to write a chimera script to automate the process of calculating the relative exposure of residues as per this tutorial: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html >>> >>> The script I have is as follows: >>> rc('surface') # defines areaSES of residues >>> rc('defattr C:/Users/Admin/Downloads/areaSESgxg.txt log 0') # define attribute using areaSESgxg.txt >>> for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): >>> for r in m.residues: >>> r.relSESA = r.areaSES/ r.areaSESgxg >>> >>> However, when I run this script, I am receiving this error: >>> <Outlook-1he3xhiv.png> >>> When I run the process using the UI I can successfully calculate relSESA >>> By using the command: "surface" >>> Then using the assign attribute function to assign areaSESgxg.txt >>> Followed by using the calculate attribute function to calculate per residue: residue.areaSES/ residue.areaSESgxg >>> >>> Could you advise on any methods I could use to fix this script to produce the output I am receiving from the UI. >>> >>> Kind regards, >>> David >>> _______________________________________________ >>> 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 > > > _______________________________________________ > 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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Save a new map with trimmed zones (vop zone command)
by Steven Truong 24 Feb '21

24 Feb '21

Dear ChimeraX Admin., Hello, I was hoping for some help on the save function for an electron-density map (.mrc file). I have a density map (#0) that I trim using: vop zone #0 nearAtoms #1 range 6 Essentially, I want to remove all the electron density that is not close to my structure (.pdb) #1. Anything farther than 6 angstroms disappears, as expected. However, when I proceed to do: save newmap.mrc #0 I get the original map with the electron density I don’t want anymore. It doesn’t seem like I can save the changes to the map, even though I see the changes in the interface. It seems to want to save everything, ignoring the vop command. Is there something else I’m missing here? Thank you for your help, Steven Truong Cambridge University sdt45(a)cam.ac.uk<mailto:sdt45@cam.ac.uk>

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Generate the .dssp file in ChimeraX ?
by Gupta, Arun 24 Feb '21

24 Feb '21

Hi, Can we generate the .dssp file output using ChimeraX based on my PDB structure as an Input.. 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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.chimerax and PhosphoSitePlus
by Daniel Gurnon 24 Feb '21

24 Feb '21

Hi all, I'm interested in visualizing post translational modified positions in Chimera or ChimeraX, using the script generated by PhosphoSitePlus (PSP). I'm not able to get it working though, so I hope you can help: Here's an example of a page with an available Chimera script. <https://www.phosphosite.org/proteinAction.action?id=4103&showAllSites=true> >From what I read in the documentation <https://www.rbvi.ucsf.edu/chimera/1.10/docs/webservices.html> about web services, I should be able to click the script, and it will open in a locally running instance of Chimera. However, in Chrome, my only option is to download the script. When I download and then try to open the script in ChimeraX (v 1.1), it tells me the ".chimerax" file type is not recognized. When I try to open it in the original Chimera (v1.15), I get the infinite spinning wheel of rainbows. These things occur whether or not I have the reference PDB structure loaded. Just to see what would happen, I also tried pasting the first command from the .chimerax file (*setattr a label Ser-89 :88.A@OG*) into Chimera and ChimeraX. The command executed successfully in Chimera, but in ChimeraX, I get the error setattr a label Ser-89 :88.A@OG Expected a keyword Thanks in advance for the assistance, Dan ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135

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"No known/registered attribute seq_conservation" in conservation tutorial
by Etowah Adams 23 Feb '21

23 Feb '21

Hi all, I am following the coloring sequence by conservation tutorial <https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-…> but ran into some unexpected behavior. I used the the exact commands, but when I ran the "color byattribute seq_conservation" command, I got an error, "No known/registered attribute seq_conservation." The association was successful so I don't know why the seq_conservation attribute is not being set. See below for the log of my commands. I also tried using my own structure and msa but ran into the same "No known / registered attribute seq_conservation" issue, despite associating with 0 mismatches. Am I somehow missing something, or is something wrong? I am using a version of ChimeraX downloaded in November 2020, running on Windows 10. > *open 121p* *121p title:* > Struktur und guanosintriphosphat-hydrolysemechanismus des C-terminal > verkuerzten menschlichen krebsproteins P21-H-ras [more info...] > > Chain information for 121p #1 > Chain Description > A H-ras P21 protein > Non-standard residues in 121p #1 > GCP — phosphomethylphosphonic acid guanylate ester > MG — magnesium ion > 121p mmCIF Assemblies > 1 author_defined_assembly > > *hide solvent* > *style ligand ball* Changed 32 atom styles > *open > https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.… > <https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.…>* > Summary of feedback from opening // > www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln fetched from https > notes Fetching 121p-consurf(1).aln from > https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.… > Downloaded 121p-consurf.aln to C:\Users\selua\Downloads\121p-consurf(1).aln > Alignment identifier is 121p-consurf(1).aln > Associated 121p chain A to Input_pdb_SEQRES_A with 0 mismatches > Opened 150 sequences from 121p-consurf(1).aln > *color byattribute seq_conservation* No known/registered attribute seq_conservation > [image: image.png] Thanks for any help, Etowah

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Fwd: Help with new user to ChimeraX training
by Elaine Meng 23 Feb '21

23 Feb '21

> Begin forwarded message: > > From: Dale Calleja <calleja.d(a)wehi.edu.au> > Subject: Help with new user to ChimeraX training > Date: February 22, 2021 at 7:46:56 PM PST > To: "chimerax(a)cgl.ucsf.edu" <chimerax(a)cgl.ucsf.edu> > > Hi there, > > My name is Dale and I’m new to using ChimeraX. Currently I’m trying to use the ‘getting started’ guide for Chimera but a lot of the commands don’t seem to work in my version of ChimeraX (0.93). The most recent example was trying to use the example commands for labelling all lys residues in the hot pink colour. From the ‘Working with commands – Part 1’ part of the guide, the command is color hot pink :lys. I always get the error Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword. > > Can you please explain why this is? Am I copying the command wrong from the ChimeraX user guide? > > Thanks in advance! > > Dale. Hi Dale, (For future reference, the correct e-mail address for asking ChimeraX questions is chimerax-users(a)cgl.ucsf.edu, CC'd on this reply.) Chimera and ChimeraX are two different programs. You cannot just use Chimera commands in ChimeraX. See the ChimeraX User Guide: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html> ... and ChimeraX tutorials: <https://www.rbvi.ucsf.edu/chimerax/tutorials.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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Re: [chimerax-users] Move atoms
by Elaine Meng 22 Feb '21

22 Feb '21

> On Feb 21, 2021, at 11:40 PM, Ruben Meerman <rubenmeerman(a)me.com> wrote: > > I am trying to use the move command to move all the atoms of a single DNA nucleotide, but the whole model moves: > > move x 3 5 model #1 atoms #1/a:44 > > The PDB model I’m testing the command on is 6BY7 (a DNA nano barrel) > > Am I doing something wrong, or just dopey? > Kind regards, > Ruben > > ps my ultimate aim is to a set of commands to untwist and unzip DNA using the move and roll commands… not sure if that’s a bit too ambitious Hi Ruben, I'm CC-ing the list, but yes in general please do send the question to the list in the first place unless it includes data that you have to keep private. The "model #1" option says to move all of model #1. Omit that if you only want to move the atoms. Also it looks like you have an extra number in there (3 or the 5). Maybe something like: move x 5 atoms #1/A:44 "move" manual page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> Structure 6by7 does not have a chain A, so you'd need a different command than the above for that specific structure. However, it sounds very difficult to untwist DNA using rigid-body movements of sets of atoms. Here are a couple of other ideas, but they are just ideas (don't know whether either one would work well) and would also take some effort to try. (1) use "torsion" command instead <https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html> (2) build a separate completely untwisted version (not available in ChimeraX, maybe via other programs, or in ChimeraX by using "torsion") and then use "morph" to morph between the twisted and untwisted <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.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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ChimeraX Python Scripting for EM Maps
by Steven Truong 22 Feb '21

22 Feb '21

To whom it may concern, Hello! I was hoping to ask for some help in Python Scripting in ChimeraX. Specifically, I am trying to fit structure files (.PDB) to electron density maps (.MAP). Is there a way to do this in .PY scripts in ChimeraX? I can’t seem to find such a command like “fitmap” in the documentation here (https://www.cgl.ucsf.edu/chimerax/docs/devel/modules.html) Additionally, it seems like the “Read and Write PDB Files” page (https://www.cgl.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/pdbio.html) of the documentation page hasn’t been updated. Is there another place that outlines how to save structures? Thank you, Steven Truong sdt45(a)cam.ac.uk Cambridge University

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Re: [chimerax-users] Issue with ChimeraX
by Tom Goddard 19 Feb '21

19 Feb '21

Hi Anas, Thanks for submitting the bug report https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4273 Your 13 inch MacBook Pro (model 16,2) uses Intel graphics. The fix for wrong (noisy) silhouette edges and selection highlights I put in a while ago only applies to Radeon graphics so it is not surpising that the daily build does not fix it. I have not seen this problem on Intel graphics before, but it may be new in macOS 11.2.1 (Big Sur). Try this ChimeraX command and see if it fixes the silhouettes graphics quality colordepth 16 This will force ChimeraX to render the silhouettes entirely off-screen which may fix the issue which I believe is an incompatibility between the framebuffer fomats between the on-screen and off-screen rendering. Tom > On Feb 19, 2021, at 10:10 AM, Anas Khawaja <anas.khawaja(a)ki.se> wrote: > > Thank you Tom for the reply. I have reported the bug as you mentioned with said description. Previously, I did try ChimeraX daily build but the same problem persisted. I installed it again just now, but I am having the same issue. Kindly let me know what I need to change to resolve the problem. Thanks > > Anas. > >> On 19 Feb 2021, at 18:50, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Anas, >> >> I think I fixed this in the ChimeraX daily build some time ago. Please get the daily build from the Downloads page and try that. On Mac laptops, a few graphics cards AMD Radeon Pro Vega and AMD Radeon Pro 5500M are doing something weird causing ChimeraX outlines not to be correct. I think it is a mismatch between either the onscreen and offscreen depth buffer formats or multisampling. >> >> In any case, can you use ChimeraX 1.1.1 menu Help / Report a Bug and just say "silhouettes look wrong" and attach the image you just sent. This will tell me exactly what Mac model and what graphics you are using, which will let me know if I have to improve my fix for the problem. >> >> Tom >> >> >>> On Feb 19, 2021, at 7:12 AM, Anas Khawaja <anas.khawaja(a)ki.se <mailto:anas.khawaja@ki.se>> wrote: >>> >>> Hello, >>> >>> I am a postdoc research fellow at Karolinska Institute, Stockholm, Sweden. I have been using ChimeraX for quite sometime. I recently updated my MacBook (macOS Big Sur, version 11.2.1) and installed the latest version of Chimera X (version: 1.1.1). I am having an issue with the ChimeraX. Whenever I use graphics silhouettes on a model protein structure, it gives me tiny boxes all over the whole structure. Apparently, without graphics silhouettes the image is fine. It does the same when I use graphics silhouettes with the density map (surface representation with opacity). I am sending an image in attachment so you know how it is. I have tried reinstalling but the problem persists. Kindly let me know asap what is needed to make the software run normally. Thanks a lot for the help. >>> >>> Best regards, >>> Anas. >>> <chimeraX.png> >>> >>> >>> När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fki.se%2Fm…>. >>> >>> Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here <https://ki.se/en/staff/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 <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl…> >

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Issue with ChimeraX
by Anas Khawaja 19 Feb '21

19 Feb '21

Hello, I am a postdoc research fellow at Karolinska Institute, Stockholm, Sweden. I have been using ChimeraX for quite sometime. I recently updated my MacBook (macOS Big Sur, version 11.2.1) and installed the latest version of Chimera X (version: 1.1.1). I am having an issue with the ChimeraX. Whenever I use graphics silhouettes on a model protein structure, it gives me tiny boxes all over the whole structure. Apparently, without graphics silhouettes the image is fine. It does the same when I use graphics silhouettes with the density map (surface representation with opacity). I am sending an image in attachment so you know how it is. I have tried reinstalling but the problem persists. Kindly let me know asap what is needed to make the software run normally. Thanks a lot for the help. Best regards, Anas. [cid:EA8EC179-1591-4C3B-AE48-AEE81A4FC329] N?r du skickar e-post till Karolinska Institutet (KI) inneb?r detta att KI kommer att behandla dina personuppgifter. H?r finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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install on debian
by Francesco Pietra 18 Feb '21

18 Feb '21

Regrettably, even here ubuntu is implicitly taken as the standard for .deb packages, while ubuntu is not compatible with debian. Therefore, which ubuntu deb package, if any, is suitable to install chimerax on debian 10? thanks francesco pietra

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Re: [chimerax-users] [Chimera-users] Installing chimerax linux
by Greg Couch 18 Feb '21

18 Feb '21

This question is better answered on the chimerax-users mailing list. Debian 10's codename is Buster. The Ubuntu versions that are based on Buster are 18.04, 18.10, 19.04, and 19.10. So I'd recommend trying the ChimeraX release for Ubuntu 18.04. If you were using Debian 9, aka Stretch, try the Ubuntu 16.04 release, and if you are using Debian 11, aka Bullseye, try the Ubuntu 20.04 release. And please let us know if it works or not. The most likely problem is a dependency on a package that is only in Ubuntu. And it would be good to know if that is the case or not. -- Greg On 2/18/2021 8:15 AM, Francesco Pietra wrote: > Hello > I would like to change to chimerax, installing it on Debian (10 Buster) > > Regrettably, it has become practice to refer to ubuntu when .deb > packages are concerned. I would appreciate being informed which u. > version, if any, is suitable for Debian 10 > > thanks > francesco pietra > > _______________________________________________ > 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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volume flip
by Boyer, Joshua A 18 Feb '21

18 Feb '21

Hello, I am new to chimera and trying to flip the handedness of a cryo density map. I have opened the *.mrc file in chimera and its current ID # is 1. It seems I should use the command 'vop zflip #1' based on the online documentation I could find. The error output says: "Expected a density maps specifier or a keyword". I am running the current ChimeraX (daily). Apologies if I am missing something simple, but I could use some assistance. Thank you in advance. ~J

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Sequence specification for comparative modelling
by Haselbach,David 17 Feb '21

17 Feb '21

Hi, I am trying to make a comparative model using modeler. I downloaded my sequence from uniprot and a homolog protein from the pdb. I associated the sequence with the homologe and the alignment is okay however there are definitely regions where there is no match at all. So when I run modeler it fails with the following output: get_ran_648E> Alignment sequence does not match that in PDB file: 1 ./6opc_1.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one-letter code matches (e.g. B to N, Z to Q). I have been trying to figure out how exactly to specify the chain IDs and residue numbers but I really didn’t get it. May I ask you to provide an example please? Best, David

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Save image error
by Zhe Wang 17 Feb '21

17 Feb '21

Hi, I am trying to generate an image for a tomogram (1.6G). It can run through if I use a value that produces 33651412 triangles. But if I use my target level value, it will need 825273846 triangles and it threw the following error: (I am wondering if this is an edge case and how should that be dealt with if I want the image at my target level value?) Many thanks, Zhe PS: MacOS 11.01.1 with ChimeraX 0.9 Executing: save image test.map_z.jpeg supersample 3 width 1200 height 1200 Traceback (most recent call last): File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ChimeraX_main.py", line 734, in init commands.run(sess, 'open %s' % arg) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2632, in run result = ci.function(session, **kw_args) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 64, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/models.py", line 604, in open session, filenames, format=format, name=name, **kw) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/io.py", line 477, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/io.py", line 431, in open_data models, status = open_func(*args, **kw) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/scripting.py", line 115, in open_command_script run(session, text) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2632, in run result = ci.function(session, **kw_args) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/commands/save.py", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/io.py", line 213, in export result = self.export_func(session, path, **kw) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/image.py", line 150, in save_image transparent_background=transparent_background) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/graphics/view.py", line 434, in image self.draw(c, drawings, swap_buffers = False) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/graphics/view.py", line 162, in draw self._draw_scene(camera, drawings) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/graphics/view.py", line 192, in _draw_scene shadow, multishadow = self._compute_shadowmaps(opaque_drawings + transparent_drawings, camera) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/graphics/view.py", line 541, in _compute_shadowmaps shadow_enabled = r.shadow.use_shadow_map(camera, drawings, self._shadow_bounds) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/graphics/opengl.py", line 1272, in use_shadow_map draw_depth(r, sdrawings, opaque_only = not r.material.transparent_cast_shadows) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/graphics/drawing.py", line 1413, in draw_depth draw_opaque(r, drawings) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/graphics/drawing.py", line 1394, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/graphics/drawing.py", line 1405, in _draw_multiple d.draw(renderer, draw_pass) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/graphics/drawing.py", line 698, in draw self.draw_self(renderer, draw_pass) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/graphics/drawing.py", line 705, in draw_self self._draw_geometry(renderer, opaque_only = any_transp) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/graphics/drawing.py", line 770, in _draw_geometry ds.draw(self.display_style) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/graphics/drawing.py", line 1575, in draw eb.draw_elements(etype, ni) File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/graphics/opengl.py", line 2483, in draw_elements GL.glDrawElementsInstanced(element_type, ne, GL.GL_UNSIGNED_INT, eo, ninst) File "src/latebind.pyx", line 32, in OpenGL_accelerate.latebind.LateBind.__call__ File "src/wrapper.pyx", line 318, in OpenGL_accelerate.wrapper.Wrapper.__call__ File "src/wrapper.pyx", line 311, in OpenGL_accelerate.wrapper.Wrapper.__call__ File "/nfs/public/rw/pdbe/httpd-em/software/chimerax/opt/UCSF/ChimeraX/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg/OpenGL/platform/baseplatform.py", line 409, in __call__ return self( *args, **named ) File "src/errorchecker.pyx", line 53, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1281, description = b'invalid value', baseOperation = glDrawElementsInstanced, pyArgs = ( GL_TRIANGLES, 2475821538, GL_UNSIGNED_INT, None, 1, ), cArgs = ( GL_TRIANGLES, 2475821538, GL_UNSIGNED_INT, None, 1, ), cArguments = ( GL_TRIANGLES, 2475821538, GL_UNSIGNED_INT, None, 1, ) ) ReplyForward

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Coloring Atoms by Hydrohpobicity and Electrostatic potential
by Y. Mutum 16 Feb '21

16 Feb '21

Hi I tried looking up on colouring atoms by hydrophobicity/ electrostatic potential, but couldn't find a way to work in my current model. So, please excuse me if this is redundant. I am working with a pdb: 6j5k and was thinking of a way to color the atoms by hydrophobicity. From this, the idea is to also use this atomic model to color a map (a cryoEM map MRC format) based on hydrophobicity, using the command 'color zone'. First, I tried to generate a 'mlp' using the command: >>> mlp #1 map true color true Even after saving the volumes in .mrc format, I am not sure how to load them up to 'color the atoms by hydrophobicity'; the command 'color sample' only seems to accept the surfaces for colouring. I also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it. Also, there are lots of subunits/ chains, so is there a more straightforward way to load these hydrophobic-potential-maps later and color the atoms by hydrophobicity? In this particular case, I am trying to color the 'whole' pdb model and the cryo-EM map by hydrophobicity EMD-0667<https://www.emdataresource.org/EMD-0667>. Any workaround suggestions would be helpful for electrostatic too. Thanks Yaikhomba

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Double and triple bond sticks
by Ruben Meerman 16 Feb '21

16 Feb '21

Dear ChimeraX, Greetings from Australia. I use ChimeraX animations to teach elementary school children how food is converted into the CO₂ we exhale, so: A) thank you for this invaluable resource B) is there any way to display double and triple bonds? And, if not, are you planning to add this feature in future versions? C) apologies for repeating this question - originally asked by Chase Smith (28 November 2019) - but I couldn’t find a response Many thanks in advance, Ruben ______________________ Ruben Meerman M: 0414 680 271 E: rubenmeerman(a)me.com

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win10 chimeraX1.1 cannot open after adding a RAM to computer
by Jianping Wu 14 Feb '21

14 Feb '21

Hi all, I cannot open chimeraX1.1 in my PC after I adding a memory to the computer (Win10 system). All other programs in my PC are not affected. The GUI just did not show up after I click the icon. There was no error message. The wired thing was even after I removed the added memory, I still cannot open it. Re-installation of chimeraX was also not helpful. Can anyone help me with it? Thanks a lot! Jianping

2 2