- ChimeraX-users - RBVI Mailing Lists

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

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Replacing regular residues with unusual ones
by anaa2 14 Feb '21

14 Feb '21

Hi, In ChimeraX can a regular residue be replaced with an unusual one using the swapaa function(pdb code 2MR)? Best wishes, Noor

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Refreshing ChimeraX - ChimeraX slows down after surface generation
by Y. Mutum 13 Feb '21

13 Feb '21

Hi I am currently using the ChimeraX Daily version - UCSF ChimeraX version: 1.2.dev202102050202 (2021-02-05). I am working with the pdb: 6j5k - a slightly large protein. If I 'hide atoms' and only 'show cartoons', I can navigate the protein visualisation using my mouse quite well - rotations, translations, zooming etc. However, once I generate the surface and then adjust the slider-side-view to adjust the views to visualise certain aspects of the protein, I have noticed that the computer becomes exceedingly slow to render even small rotations using the mouse - I can understand that this might be because the protein is big. However, the next part - if the surfaces were now deleted and only cartoons are shown in the same session (as in the beginning), the computer is exceedingly slow for mouse work - rotations, translations, slider-view etc. Is there some way to refresh and regain back this agility and remove this hysteresis? The only workaround seems to be to close ChimeraX and then reopen it again, but this is not slightly more tedious if we have to close and reopen every time I make a surface. The commands I have used are: open 6j5k; hide atoms; show cartoons surface #1 enclose #1 Then try to navigate... ~surface; show cartoons And then navigating again.... If there could be some work-around, or a new fix in the ChimeraX_version, it would be really helpful for working with large proteins seamlessly. Thanks Yaikhomba

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Re: [chimerax-users] [Chimera-users] how to color an model by an attribute in chimerax
by sunyeping 10 Feb '21

10 Feb '21

------------------------------------------------------------------ From:孙业平 <sunyeping(a)aliyun.com> Send Time:2021年2月3日(星期三) 16:09 To:ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject:Re: [chimerax-users] [Chimera-users] how to color an model by an attribute in chimerax Hi Elaine, Thank you for you help. I will send chimerax questions to chimerax mail list next time. By changing the match mode from "1-to-1" to 'any', I can also color the protein according to the entropy.txt file. If you recheck the entropy.txt file you will find that there are quite a few residues have an entropy vavle around 0.3, in addition to the 0.788 residue. Could you tell me how to generate a color gradient bar base on the entropy values in the entropy.txt file in chimerax? Best regards, Yeping ------------------------------------------------------------------ From:Elaine Meng <meng(a)cgl.ucsf.edu> Send Time:2021年1月28日(星期四) 00:44 To:孙业平 <sunyeping(a)aliyun.com> Cc:ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject:Re: [Chimera-users] how to color an model by an attribute in chimerax Hi Yeping, **Please send ChimeraX questions to the chimerax-users(a)cgl.ucsf.edu address, *not* to chimera-users(a)cgl.ucsf.edu, because that makes people confused about which program we are talking about. Two more thoughts about your file: (1) you need to make sure the residue numbers in the file all match to your structure. I don't know which structure you are using so when I test it on some other structure that doesn't have all the same residue numbers, it does not work unless I change the match mode from "1-to-1" to "any". You might want to try using match mode "any". (2) looks like one residue has a high value 0.788 and all the others are very close to zero, so when I color the whole range the structure is all the same color (used for the low end) except for the one high-value residue. E.g. coloring by attribute entropy using palette blue-white-red makes the whole structure blue except for one residue red. Elaine > On Jan 27, 2021, at 8:25 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Sun Yeping, > To use the "open" command to open defattr format you need ChimeraX daily build from Oct 30, 2020 or newer. Or if you are using ChimeraX 1.1, you can use the "defattr" command to open the file. Older ChimeraX than version 1.1 cannot read this file type at all. Changes and approximate dates are given in the Change Log: > > <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> > > The format is described here: > <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.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 27, 2021, at 1:04 AM, sunyeping <sunyeping(a)aliyun.com> wrote: >> >> Dear Elaine, >> >> Thank you for your reply. The attribute file entropy.txt is available at >> >> https://drive.google.com/file/d/1oG0O4zKqw-uD5SeLTrAu16c3Jh8m3LG5/view?usp=… >> >> Could you please help check whether the format is correct"? >> >> I cannot figure out how to open this attribure file in chimera. When I input "open entropy.txt format defattr" in chimerax, I get the following error message: >> >> Invalid "format" argument: Should be one of 'aln', 'amira', 'apbs', 'bild', 'brix', 'ccd', 'ccp4', 'cellpack', 'cmap', 'cmd', 'collada', 'compiled python', 'cube', 'dcd', 'delphi', 'dicom', 'dock', 'dsn6', 'dv', 'emanhdf', 'fasta', 'fsc', 'gltf', 'gopenmol', 'hdf', 'hssp', 'html', 'ihm', 'images', 'imagic', 'imod', 'imodmap', 'ims', 'macmolplt', 'markers', 'mmcif', 'mmtf', 'mol2', 'mrc', 'msf', 'netcdf', 'obj', 'pdb', 'pdbqt', 'pfam', 'pif', 'pir', 'positions', 'priism', 'profec', 'pseudobonds', 'python', 'rsf', 'sdf', 'segger', 'session', 'sff', 'situs', 'smiles', 'spider', 'stl', 'stockholm', 'storm', 'swc', 'tom_em', 'trr', 'uhbd', 'uniprot', 'vtk', 'web fetch', 'xplor', or 'xtc' >> >> Could you tell me what is the correct way to open the file? >> >> Thank you, >> Best, >> Yeping >> ------------------------------------------------------------------ >> From:孙业平 <sunyeping(a)aliyun.com> >> Send Time:2021年1月26日(星期二) 11:53 >> To:chimera-users <chimera-users(a)cgl.ucsf.edu> >> Subject:[Chimera-users] how to color an model by an attribute in chimerax >> >> Dear all, >> >> I wish to color an model by an attribute in chimerax. The attribute is the entropy which is calculted by an external software. I wrote the entropy values of each residue in a text file (attr.txt) like the following: >> >> attribute: entropy >> match mode: 1-to-1 >> recipient: residues >> :1 0.0 >> :2 0.0014948 >> :3 0.0090952 >> :4 0.0004805 >> :5 0.1102497 >> :6 0.0095258 >> :7 0.0008226 >> :8 0.0042205 >> :9 0.0037255 >> :10 0.0006678 >> :11 0.0027988 >> :12 0.0193925 >> :13 0.0153925 >> :14 0.0052115 >> :15 0.0020136 >> .......... >> >> However, when I input the command "color byattr attr.txt", I get the following error information: >> "No known/Registered attribute attr.txt" >> >> Could anyone tell me what is the correct way to do this? >> >> With many thanks. >> >> Best regards >> > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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How to view SwissDock output in ViewDockX
by Tom Goddard 10 Feb '21

10 Feb '21

On Feb 9, 2021, at 3:56 AM, Michael Weber wrote: Hi, ... I use SwissDock for molecular docking experiments and there is an explanation on how to examine the output results in Chimera. Unfortunately all those workflows appear not to work in ChimeraX - are there any plans (or even already existing documentation which very well might have escaped my attention) to get these working in ChimeraX as well? Invoking ViewDockX from either the menu >tools>general>ViewDockX or by typing the command after having loaded a PDB structure plus the docked ligands just results in the message "No suitable models found for ViewDockX".

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clear gallery of previous pdb files?
by Elghobashi-Meinhardt, Nadia 08 Feb '21

08 Feb '21

Dear ChimeraX help, Is there any way to clear the gallery view of all previous pdb files if it is getting too cluttered? Thank you! Nadia ----------------------------------------------- Dr. Nadia Elghobashi-Meinhardt Biomolecular Modeling Institute of Chemistry Technical University Berlin Straße 17. Juni 135 10623 Berlin

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