- ChimeraX-users - RBVI Mailing Lists

Question about processing of multi-model PDB
by Enrico Martinez 23 Sep '24

23 Sep '24

Dear Chimera-X users ! I am working on the processing of a multi-model pdb file containing biological assembly of the dimeric protein. Precisely, every monomer is in a separate model with the same chain ID (A). I need to rename the chain A to chain B in the second model and then fuse the both models, so that the entire construction will be in the same model. What commands could be used to such modifications? Many thanks in advance Enrico

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Identify Contacts?
by Shawn Rumrill 23 Sep '24

23 Sep '24

Hello ChimeraX Users, I would like to analyze protein/nucleic acid complexes from the PDB by comparing the protein/nucleic acid chain interactions in each. Ideally I would like to know: * The number of interactions < 4.0 A that the nucleic acid makes with neighboring protein chains * If possible, output a list of those interactions to a text file * Even better, generate a 2D interaction map I tried contacts (#1/A | #1/B) #1/C cutoff 4.0 saveFile contacts_ABC.txt for the first bullet (with a few permutations when it didn't work), but received the error "expected a keyword." Has anyone successfully determined something like this in ChimeraX? Thanks for the input! Shawn R Rutgers University

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Re: [Chimera-users] Generating a single electrostatic potential surface for a protein + ligand complex
by Elaine Meng 22 Sep '24

22 Sep '24

Hi Jade, This chimera-users email address is for questions about Chimera. In the future, for questions about ChimeraX, please instead use the other address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (CC'd on this message) to avoid confusing other users. This answer is for ChimeraX and does not apply to Chimera: If you meant you wanted a single surface that goes around both the ligand and the protein in a single blob: You would have to use the "surface" command with the "include" option to make a single surface around both the ligand and the protein. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options> Then you would have to use "coulombic" command with the "surfaces" option to use the surface you already made instead of one that has the protein only. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coulombic.html#charges> Example commands for PDB file 8iyx with GPR34 receptor with antagonist bound, residue name S6R. This example assumes you want to see the potential that is from both the receptor and the ligand, on the surface that is both the receptor and the ligand. open 8iyx surface include protein | :S6R coulombic protein | :S6R surfaces #1.2 The surface command says to make a single blob around both protein and residue S6R (the symbol between them is a vertical bar character). The coulombic command says to calculate the electrostatics using the charges of both the protein and residue S6R, and use it to color the previously made surface #1.2. You have to look in the Models panel and use the disclosure triangle to see what model number the surface has. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 21, 2024, at 11:07 PM, jadeshi88--- via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > New user to ChimeraX here, would really appreciate some help! > > I'm trying to generate an electrostatic potential surface for a protein-ligand complex. Currently, I am using the surface/coulombic, and surface ligand/coulombic ligand commands to generate surfaces separately for the protein and ligand, and then exporting to an .obj file. However, by doing so I'm left with two separate surface meshes, and what I really want is a single surface that encapsulates both entities. Is it possible to do this? > > Thanks in advance!

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Transition of the camera between two view perspectives
by Enrico Martinez 22 Sep '24

22 Sep '24

Dear Chimera-X users ! I have a question about the transition of the camera between two different views. E.g. I have (1) a closed zoom view on some selection with the defined coordinates view matrix camera 0.33173,-0.24137,-0.91197,-114.7,0.22734,0.95868,-0.17103,31.486,0.91557,-0.15059,0.3729,66.518 and (2) some general view of the whole system, with the same coordinates. Now, starting from the closed view I need to gradually move camera from (1) to the (2), which can be manually achieved using move command e.g. # zoom out and shift camera to the right move z -0.3 300; move y -0.05 300 Would it be possible additionally to provide coordinates of the both views in order to make such a camera transition more smooth and accurate ? Many thanks in advance ! Enrico

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Ligand protein interaction in visual
by Mamadou Sangare 22 Sep '24

22 Sep '24

Dear I would like to insert in my PPT presentation ten ligands (chemical compounds) interacting with the binding site of the protein with chimera X. Thank you in advance for your support Kind regards! Mamadou SANGARE, PhD student ACE-Mali

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Slight bug in ChimeraX
by Sergio Pipaón Alcíbar 19 Sep '24

19 Sep '24

Hello!! My name is Sergio Pipaón, from the National Center for Biotechnology in Madrid. I wanted to report a couple of -what I believe are- bugs: 1) I hate the depthCue to visualize my structures, so I usually run: lighting depthCue false in my sessions. However, for some reason, this is not stored in the session info, and you have to run it again every time you close and open your session. 2) The commands that you can introduce in the ’Startup’ section of the preferences seem to not work in some cases (I am referring to the ‘Execute these commands at startup’ text box). The aliases work fine, but I also have written the following: graphics silhouettes true lighting soft lighting shadows true lighting depthCue false ~cofr And these do not seem to run. Definitely not the lighting depthCue false. Extra: I would be cool to have a button in ‘Graphics’ to easily change the depthCue from to true to false. Am I obsessed with the depthCue? Maybe, but I hope that this is valuable feedback. I am currently running ChimeraX-1.8-rc2024.05.10. Thank you guys!! Sergio. -- Sergio Pipaón Alcíbar (PhD Student) Dept. of Macromolecular Structures, lab. S0 / Ext: 5347 National Center for Biotechnology (CNB - CSIC) C/ Darwin, 3 28049, Cantoblanco-Madrid email: spipaon(a)cnb.csic.es

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Re: [Chimera-users] Selecting chain via command line
by Elaine Meng 19 Sep '24

19 Sep '24

Hi Ellen, You sent this question to the Chimera address -- in the future, please send ChimeraX questions to the ChimeraX address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here to avoid confusing the other users. This answer is for ChimeraX: It works for me: labels show the insertion code. Make sure you have ChimeraX 1.8 or newer. Example 1h4w which has residues with insertion codes 184A, 188A, 221A: open 1h4w label :184,184A height 2 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 17, 2024, at 10:20 PM, Ellen Shrock via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine and Eric, > > I hope all is well. I am writing because I am using the chimerax command 'label sel residues height 1' but I noticed that the insertion codes are not making it into the labels. I attached an example cxc session along with the commands provided. In, for example, model #4, there are two residues labeled '100' even though when I hover over the residues, they have insertion codes. Do you know if there is a way I can label the residues with the position numbers including the insertion codes? > (I copied below the entire script I ran. Please let me know if there is any additional information I can provide.) > > Thanks, > Ellen > >

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Displaying methyl groups on DNA?
by Maja Divjak 18 Sep '24

18 Sep '24

Hi there, Hope you're well. I'm sure this is a rookie question, but I'm having trouble displaying the methyl groups on a methylated DNA sequence, as shown in PDB 6C1Y. [A colorful structure with multiple colors Description automatically generated with medium confidence] I've tried selecting the DNA and then showing the methyl functional group, but this selects all the methyl groups including those in the protein sequence. I also tried selecting the individual bases I know are methylated using eg select #2/C:6, but not sure of the command to show the methyl group following this ie select #2/C:6 show methyl does not work, whereas show methyl as a solo command shows all methyl groups in the whole structure. Couldn't find anything in the help files, unfortunately. Thanks so much and best wishes, Maja

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(no subject)
by Kasia Ojar 18 Sep '24

18 Sep '24

Hello, I hope this email finds you well. I am writing because I have a couple of questions regarding opening up the ChimeraX program. I am a student and I have downloaded the ChimeraX and cannot seem to open the program despite it being on my desktop. I have Microsoft and the software is Windows 11. Thank you for your help.

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Missing libraries from package install ChimeraX?
by Mike King 17 Sep '24

17 Sep '24

Hi I have just installed ChimeraX 1.8 from the RedHat 8 rpm package. In our previous Chimera installs there were some libraries that don't appear to be in the 1.8 rpm distribution. For example, _multiscale.so and _chimera.so which our developers have been using, are these available via a different route for ChimeraX 1.8? Many thanks Mike Mike King Director, Scientific Computing Astex Pharmaceuticals 436 Cambridge Science Park Milton Road, Cambridge CB4 0QA, UK Tel: +44(0)1223 435095 Email: mike.king(a)astx.com Website: http://www.astx.com<http://www.astx.com/> This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately.

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