February 2021 - 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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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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ChimeraX-users February 2021