- ChimeraX-users - RBVI Mailing Lists

info distmat command
by NUR AIDA SAKINAH 27 Sep '24

27 Sep '24

Hi ChimeraX teams, Can you guide me to use the *atoms-spec* for info distmat command. I want the output in chimerax log to list out distances between drug compound and the amino acids side chains and only display the distances below than 4 A. For now, what i have got, the output include distances between atoms in the drug itself and atoms in the amino acids itself. The command that i have try are: 1. info distmat (protein & sideonly) | :dex ::num_distance< 4 2. info distmat (protein & sideonly) | :dex 3. info distmat (protein & sideonly) & (:dex) distance < 4 Hope you could help me with this. Regards with thanks, Aida.

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Atoms command spec
by NUR AIDA SAKINAH 27 Sep '24

27 Sep '24

Hi ChimeraX teams, Can you guide me to use the *atoms-spec* for info distmat command. I want the output in the chimerax log to list out distances between *the drug compound and the amino acids side chains and only display the distances below than 4A*. For now, what I have got, the output includes distances between atoms in the drug itself and atoms in the amino acids itself and I don't want that. Only display distances between atoms of the drug and the amino acids side chains. The protein and drug details: PDBID= *4YVP* with drug compound *DEX* The drug binding site distance is below than *4A*. The command that i have try are: 1. info distmat (protein & sideonly) | :dex ::num_distance< 4 2. info distmat (protein & sideonly) | :dex 3. info distmat (protein & sideonly) & (:dex) distance < 4 Hope you could help me with this. Regards with thanks, Aida.

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How to increase the font size of pseudobond labels
by Suhas Srinivasan 26 Sep '24

26 Sep '24

Dear ChimeraX Community, I was trying to increase the default font size of the very small labels displayed on the pseudobonds that are generated from the “distance” command. Selecting the pseudobond label and then using the command “label size 512” had no effect. Your help would be appreciated and thank you for your time. UCSF ChimeraX 1.8 macOS 14.7

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ChimeraX download problem
by Sophie Scobell 25 Sep '24

25 Sep '24

Hi, I've been trying to download ChimeraX on my personal computer for the past two weeks and keep getting this error message: "Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error. More information about this error may be available in the server error log." I'm using a Mac and I've tried the MacOS download on both Safari and Chrome with the same issue. Any advice would be greatly appreciated, Thank you! Sophie

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Re: Inquiry: Selecting Individual Electron Density Maps for Comparative Analysis
by Tom Goddard 25 Sep '24

25 Sep '24

Hi Yan, PDB 4ola is an X-ray structure so you could fetch PDB and the X-ray map (from the Electron Density Server) using ChimeraX commands open 4ola open 4ola from EDS The map is a unit cell and does not cover the PDB atom coordinates. To use the crystal symmetry to extend the map to cover the atom coordinates use ChimeraX command volume cover #2 atomBox #1 The x-ray map of course has other copies of the molecules packed together and if you want to see just the x-ray density near the atom coordinates you could use volume zone #3 near #1 range 3 For PDB 7sva which is a cryoEM structure with map at the EMDB with id 25446 you can open both with open 7sva open 25446 from emdb Converting the PDB files to maps gives a different result than looking at experimental results, and I'm not sure why you want to do that. But the ChimeraX molmap command will do that by adding up Gaussians at the atom positions. That does not give a good approximation to the experimental maps in most cases. All these commands are fully documented in the ChimeraX User Guide. Tom > On Sep 25, 2024, at 1:54 AM, Yan ZHANG 张艳 <zhangyan30(a)westlake.edu.cn> wrote: > > Hi Tom, > > Thank you for your response. I'll try to explain my situation more clearly. > > I am comparing two structures (PDB IDs: 4ola and 7sva). I want to use the "color near atoms" feature in ChimeraX to color the maps of both structures. However, 4ola is a crystal structure and is in MTZ format. I would like to display it in the same way as an MRC file. > > I hope this is clearer. My current solution is to convert the PDB file of 4ola to an MRC file directly. This approach seems to work, but I am unsure if it is acceptable. > > Thank you for your help. > > Best regards, > Yan > > 发件人: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > 日期: 星期三, 2024年9月25日 14:16 > 收件人: Yan ZHANG 张艳 <zhangyan30(a)westlake.edu.cn <mailto:zhangyan30@westlake.edu.cn>> > 抄送: chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > 主题: Re: [chimerax-users] Inquiry: Selecting Individual Electron Density Maps for Comparative Analysis > > You don't often get email from goddard(a)sonic.net <mailto:goddard@sonic.net>. Learn why this is important <https://aka.ms/LearnAboutSenderIdentification> > Hi Yan, > > We might have advice if you can explain what you are doing more clearly. MRC files are real space maps and MTZ files contain Fourier space coefficients. > > Tom > > > On Sep 24, 2024, at 9:57 PM, Yan ZHANG 张艳 via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > Dear ChimeraX Team, > > I hope this message finds you well. > > I am writing to inquire whether it is possible to selectively choose individual electron density maps of a single model from the MTZ files containing crystallographic data. This capability would enable me to perform comparative analyses of the same structure obtained through different methods. Currently, I am facing a challenge as the MRC files cannot be aligned with the MTZ files. I am seeking your guidance on whether there is a solution or tool within ChimeraX that can assist me in this process. > > Your expertise and support in this matter would be greatly appreciated. I am looking forward to hearing from you at your earliest convenience. Thank you very much for your attention to this inquiry. > > Best regards, > > Yan Zhang > Westlake University > Email: zhangyan30(a)westlake.edu.cn <mailto:zhangyan30@westlake.edu.cn> > > > > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

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Ball representation for protein-ligand system
by Enrico Martinez 25 Sep '24

25 Sep '24

Dear ChimeraX users ! I've just found a small bug in the protein-ligand representation. if I try to change the representation of ball and sticks using: style protein ball size protein ballScale 0.18 it changes the ball representation for the both protein and ligand (e.g. defined as :lig in the system). While there is not problems with sticks: size protein stickRadius 0.12 size :lig stickRadius 0.18 So it can be applied selectively on the both selections Many thanks in advance for any suggestions ! Enrico

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Inquiry: Selecting Individual Electron Density Maps for Comparative Analysis
by Yan ZHANG 张艳 24 Sep '24

24 Sep '24

Dear ChimeraX Team, I hope this message finds you well. I am writing to inquire whether it is possible to selectively choose individual electron density maps of a single model from the MTZ files containing crystallographic data. This capability would enable me to perform comparative analyses of the same structure obtained through different methods. Currently, I am facing a challenge as the MRC files cannot be aligned with the MTZ files. I am seeking your guidance on whether there is a solution or tool within ChimeraX that can assist me in this process. Your expertise and support in this matter would be greatly appreciated. I am looking forward to hearing from you at your earliest convenience. Thank you very much for your attention to this inquiry. Best regards, Yan Zhang Westlake University Email: zhangyan30(a)westlake.edu.cn<mailto:zhangyan30@westlake.edu.cn>

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Apply the user's rotation in Python
by Roden Deng Luo 24 Sep '24

24 Sep '24

Hi, If I open a protein structure, change the right mouse to rotate, select the structure, rotate it by the right mouse, and then execute the following script in the Python Shell, the structure will be moved; see the video ( https://i.gyazo.com/d72344f9c8610298f574c23e53224aac.mp4) I would expect it to be not moved as the mol.atoms.coords have not been changed. The mol.atoms.scene_coords have been changed instead. But this could be my misunderstanding of the design intent. I encounter some bugs in the downstream analysis using scene_coords only. from chimerax.atomic import Structure mol = session.models.list(type = Structure)[0] transformation = mol.scene_position mol.atoms.transform(transformation) However, if I open the same structure again and execute the following, it will go to the user's rotation. mol_2 = session.models.list(type = Structure)[1] mol_2.atoms.transform(transformation) So, I then applied the following code in my script. As a result, everything is as expected, and there is no bug. mol_path = mol.filename transformation = mol.scene_position mol.delete() mol = run(self.session, f"open {mol_path}")[0] mol.atoms.transform(transformation) I wonder if there is a way to bypass this re-opening of the file. I am with version 1.7.1 (2024-01-23) on Win 11. Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Bond built manually with ChimeraX not shown up in Coot
by Kai Cai 24 Sep '24

24 Sep '24

Dear colleagues, I am trying to build a N-glycan into my model using 'bond' command with ChimeraX, by connecting the ND2 atom from an ASN residue to the C1 atom of the N-glycan (NAG). However, the manually built bond didn't show up when I opened the coordinates in Coot. Is there a way to overcome this issue? The bond length is 1.4 Å. Thanks in advance! Cheers, Kai ________________________________ UT Southwestern Medical Center The future of medicine, today.

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unroll the helical structure
by Dmitry Semchonok 24 Sep '24

24 Sep '24

Dear colleagues, When one has a helical structure, can it be unrolled, and can the new unrolled map be saved? Thank you. Kind regards, Dmitry

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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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MD
by SAWABE Tomoo 17 Sep '24

17 Sep '24

To whom it may be concerned, Thank you so much for developing excellent program for analyzing protein structures. I found Chimera could do molecular dynamics simulations. If I do MD to predict proton paths described in https://www.pnas.org/doi/epdf/10.1073/pnas.1706278114, please teach me which tool we can use. Best Tomoo Sawabe Hokkaido Univ.

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Error when opening session file cross-platform
by Alexander Lee 17 Sep '24

17 Sep '24

I created a python session file on ubuntu and tried to open it on windows. Ubuntu was using Chimera 1.18 build 42535 but windows was using 1.18 build 42531. I've tried updating chimera on windows, but it said I was on the latest version already. When I open it on ubuntu, it works. My session file is ~ 1.5 GB including smoothed trajectory. What should I do? Here are the outputs after running debug on windows: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions Return code: -1073741819 Press return or enter to to exit [cid:0c988132-7bb8-429c-a6c7-f91f6db3b590] [cid:55bba9bf-1168-4782-b772-4d2e36e05e97]

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Change fetch download location
by Walker Orr 13 Sep '24

13 Sep '24

Hi, I was wondering how to change the fetch download location from downloads to a custom-assigned folder. I saw how to do this on chimera, but couldn't find guidance for ChimeraX in the documentation. Is there a way to do this? Thanks, Walker

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Molmap default to cubic box?
by Oliver Clarke 13 Sep '24

13 Sep '24

Hi, Currently, molmap defaults to creating the new map in a minimal bounding box - a minimal rectangular prism. Most cryoEM software doesn't like rectangular prisms, and rather prefers cubes (ideally with sides that are an even number of voxels). Would it be possible to either (a) alter molmap so it defaults to a minimal cubic box or (b) add an option to automatically resample to a cubic box of specified dimensions? Often this doesn't really matter as we have a map already loaded that we can resample on the grid of, but it would be convenient to be able to do this in a single command. Cheers Oli

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Save Session
by F.Xavier Gomis-Rüth 12 Sep '24

12 Sep '24

Dear Elaine, I am trying to save the session under ChimeraX v. 1.8 but the program refuses to do so with the message below. Any suggestion is welcomed. Best, Xavier --

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