- ChimeraX-users - RBVI Mailing Lists

Molecular Dynamics in ChimeraX
by Enrico Martinez 30 Sep '24

30 Sep '24

Dear ChimeraX users! I noticed that in ChimeraX there is no built-in molecular dynamics simulation engine as opposed to the older UCSF Chimera. Is it possible to use some visualization trick to deform slightly static coordinates of atomic selection introducing (visually) the impression that they move during movie recording ? Many thanks in advance Enrico

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Software copyright consulting
by 姜恩誉 27 Sep '24

27 Sep '24

Hello, is the application of your Chimera X software for paper publication a non-commercial use？ Looking forward to your reply. Thank you 姜恩誉 2023111025(a)stu.njau.edu.cn

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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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Chimerax's download link is no longer working
by 卢健之 11 Sep '24

11 Sep '24

Hello, I tried to dowonload the chimerax from the link https://www.rbvi.ucsf.edu/chimerax/download.html. But it seems the server is down. I wonder if you could provide me with a new download link. I would really appreciate it.

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no template at MD forcefield
by Dmitry Semchonok 11 Sep '24

11 Sep '24

Dear Tristan and colleagues, I hope you are doing well. I have a question about the cofactors and residues that ISOLDE cannot see immediately. [cid:17de3c4d-4ac6-471b-b5b9-ecaa4e534d18] What is the proper way to treat them? The program proposes that I do a search and then give the options. Shall I select the most probable one out of the list? And how do we deal with Chlorophylls (Chl a; Chl b) and carotenoids (car)? And sometimes, even with regular ones like ARG [cid:8ff9222b-feb1-47b3-9b5e-a52e714e2355] Thank you in advance. Kind regards, Dmitry

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Select all connected atoms to selection
by Alexander Lee 10 Sep '24

10 Sep '24

Hi! I want to select all covalently bonded atoms to my selected atom. Is this possible? Currently, I'm using the command select @{atom_name}; select zone select 2 It works, but I'm worried about accidentally catching any stray unconnected atoms when doing this in batches of pdbs. Thanks!

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atoms.scene_coords inconsistency before and after saving
by Roden Deng Luo 10 Sep '24

10 Sep '24

Hi, With version 1.7.1 (2024-01-23), if I open a structure (tested with 6MEO and 6ARA), select the whole molecule, change "Right Mouse" to "Rotate model", rotate the model by dragging with the right mouse, save the model into a .cif file (uncheck "Use untransformed coordinates"), and then type the following python script in the Shell in the session performed the rotation and in a new session/launch of ChimeraX and opening of the saved file, the results are different, see the attached screenshots. ======= from chimerax.atomic import Structure mol = session.models.list(type = Structure)[0] mol.atoms.scene_coords ======= For 6ARA, if I do not change the camera setting before rotation (drag the left mouse), only rotate in the original camera setting, this is not reproduced. But if I change the camera setting, this is reproduced. For 6MEO, I always reproduce the described behavior. From https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/atomic/atomic.html#chi… , *property *scene_coords <https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/atomic/atomic.html#chi…> Atoms’ coordinates in the global scene coordinate system. This accounts for the Drawing positions for the hierarchy of models each atom belongs to. Either I misunderstood the whole scene and camera system, or this should not have happened. Why is this the case? How can I access from the session performed the rotation the coords as in a new session? 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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license for university students
by Angel David Montijo Valdés 09 Sep '24

09 Sep '24

Good afternoon, I am writing to you in the kindest way to request a free use license for the chimera X program. Because I am a student at the National Autonomous University of Mexico (UNAM), within the Faculty of Sciences, and it would be a great opportunity to use your tool in different molecular biology analyses. If you need a proof of my identity as a student, you can ask me for it without any problem. I look forward to hearing from you. Best regards.

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Select multiple rotamer conformations for a single amino acid
by Alexander Lee 09 Sep '24

09 Sep '24

Hi! I was able to select and use multiple rotamer conformations simultaneously for a single amino acid using the Rotamers tool, saved as alternate locations within a pdb file. Is there a way to do that using swapaa or from the command line?

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Ribbon style editor
by Alessio Nocentini 09 Sep '24

09 Sep '24

Hello, I have been an academic user of chimera for years. I have just downloaded chimerax but I cannot find the ribbon style editor. Can you please help? Best regards Alessio -- Dr. Alessio Nocentini University of Florence Neurofarba Department Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685 *NEUROFARBA Dipartimento di **ECCELLENZA 2023-2027*

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Re: [Chimera-users] morph command in chimerax
by Elaine Meng 09 Sep '24

09 Sep '24

Hi Bryan, Since this is a ChimeraX question, I've CC'd chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> --- in the future please use that mailing list for ChimeraX questions, because we don't want to confuse users between the two programs, for which the answers may be different. This answer is for ChimeraX: The "morph" command is for atomic structures, not maps. That's why it keeps saying you need structures! This is mentioned in the first sentence of the help page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> To instead morph maps, see the "volume morph" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph> 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 9, 2024, at 7:29 AM, Hansen, Bryan (NIH/NIAID) [E] via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > I’m using ChimeraX v 1.8 (2024-06-10) and I’m having a problem with the morph command. No matter how I format the command I’m getting the same error message of “Require at least 2 structures for morph” I’ve tried > morph #3,4 core 0.1 frames 75 wrap t > and > morph #3#4 core 0.1 frames 75 wrap t > These are 2 electron density maps so there’s no sequence info docked in yet. Thanks for any tips or advice on what I’m doing wrong. > Bryan Hansen

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MD Trajectory
by Mcguire, Kelly 06 Sep '24

06 Sep '24

What is the largest MD trajectory file (i.e. DCD) ChimeraX can handle? VMD is designed for very large MD trajectory visualization and analysis. Is ChimeraX for smaller trajectories? Kelly McGuire PhD Postdoc - Herzik Lab University of California - San Diego

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colored stl file for 3d printing
by Haydar Witwit 06 Sep '24

06 Sep '24

Dear ChimeraX team, I'd like to know if it is possible to save a colored file of pdb into stl, because when I save the file as stl, chemierax saves it as a monocolor structure. Actually, my intention was to 3d print a hydrophobic structure of small protein but labeled with one letter code label and position of the amino acids. Something similar to the following image: [cid:4c34bc91-300a-456c-8583-ab4de7f1b1d9] Kind regards Haydar

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Re: Optimizing ChimeraX Performance for Multiple Subtomo Maps
by Tom Goddard 06 Sep '24

06 Sep '24

Hi Wang, Glad to hear ArtiaX helps showing your subtomogram averaged particles. An important feature of that extension written by Utz Ermel optimizes the display of thousands of particles by not using a separate ChimeraX model for each one. I tried opening 1500 maps of size 20 x 20 x 20 grid points in ChimeraX 1.8 on a Mac Studio M2 Ultra with much less powerful graphics than an Nvidia 4090, displaying all as surfaces, full lighting, and they rotated, zoomed and translated usably fast at 9 frames per second. So I am surprised you had a problem and I don't know why it is slow for you. Tom > On Sep 6, 2024, at 3:01 AM, 王光磊 <wangguanglei20(a)mails.ucas.ac.cn> wrote: > > Hi Tom, > > > Thank you for your prompt response. > > It seems that the performance issue was caused by the excessive number of subtomo maps. In my case, I loaded approximately 1,500 subtomo maps using the subtomo2chimera script, and displayed them in surface mode. This led to ChimeraX freezing for several seconds after any rotation or zoom of the view. Loading an extra tomograph did not affect performance. > > I tried using AriaX to load the subtomo maps, and now the scene runs smoothly. Thank you for your advice! > > Thanks, > > Wang GuangLei > > > > -----原始邮件----- > 发件人:"Tom Goddard" <goddard(a)sonic.net> > 发送时间:2024-09-06 03:34:59 (星期五) > 收件人: 王光磊 <wangguanglei20(a)mails.ucas.ac.cn> > 抄送: chimerax-users(a)cgl.ucsf.edu > 主题: Re: [chimerax-users] Optimizing ChimeraX Performance for Multiple Subtomo Maps > > Hi Wang, > > I think your Nvidia 4090 should handle the large tomogram fine, and probably the slowdown is because having 1000-2000 open model of any kind, even if they are small like your subtomo maps, is more than ChimeraX was designed to handle. I am surprised though that rotating the view becomes slow because that should just move the camera which should not depend on the number of models shown. Do I understand correctly that you just open the tomogram and 1000-2000 subtomograms, display them all, and rotate and it updates slowly? How slowly, like 1 frame per second, or does it freeze for ten seconds? What display style do you use for the subtomograms, surface or volumetric? > > You might be interested in the ArtiaX ChimeraX extension which is for looking at particles in tomograms. You would get it using ChimeraX menu Tools / More Tools.... > > Tom > > >> On Sep 5, 2024, at 1:15 AM, 王光磊 via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> >> >> Hi, >> >> I'm using chimerax to display my tomograph and multiple subtomo averages in surface mode. Specifically, I need to visualize a 1440*1022*250 tomograph, along with 1000-2000 subtomo maps, sized at 32x32x32 and 16x16x16. However, loading such a large number of maps has significantly slowed down ChimeraX, particularly when rotating the view. Is there any settings to improve interactive performance or increase hardware utilization? I hope to avoid cropping the tomograph. >> >> My system specifications are as follows: >> >> Dual Intel Xeon 5317 processors(a)3.00GHz >> RTX 4090 GPU >> 128GB RAM >> Operating System: CentOS Stream 9 >> GNOME Version: 40.4 >> GPU Driver Version: 550.54.15 >> I would greatly appreciate any suggestions. >> >> Thanks, >> >> Wang GuangLei >> >> _______________________________________________ >> 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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error in the documentation?
by Bourguet,Pierre 06 Sep '24

06 Sep '24

Dear ChimeraX support, First of all, thank you for developing & maintaining such an easy-to-use software. I am not trained as a structural biologist, but I looking at more and more structures thanks to alphafold. The journey is much nicer since I switched to ChimeraX! I have noticed the following inconsistency in the documentation. https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts "If one set of entities is higher-confidence (lower in pLDDT<https://alphafold.ebi.ac.uk/faq#faq-12>) than the other, it is usually best to specify them as the aligned set so that the coloring will show the error values of the lower-confidence set." My understanding is that it should say "(higher in pLDDT)". Hopefully that helps! Best, Pierre Pierre Bourguet Postdoc Gregor Mendel Institute of Molecular Plant Biology GmbH Dr. Bohr-Gasse 3, 1030 Vienna, Austria pierre.bourguet(a)gmi.oeaw.ac.at http://www.gmi.oeaw.ac.at [cid:gmi_48f983b7-0679-4d21-99bc-bda376e5bf6b.png]

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Optimizing ChimeraX Performance for Multiple Subtomo Maps
by 王光磊 05 Sep '24

05 Sep '24

Hi, I'm using chimerax to display my tomograph and multiple subtomo averages in surface mode. Specifically, I need to visualize a 1440*1022*250 tomograph, along with 1000-2000 subtomo maps, sized at 32x32x32 and 16x16x16. However, loading such a large number of maps has significantly slowed down ChimeraX, particularly when rotating the view. Is there any settings to improve interactive performance or increase hardware utilization? I hope to avoid cropping the tomograph. My system specifications are as follows: Dual Intel Xeon 5317 processors(a)3.00GHz RTX 4090 GPU 128GB RAM Operating System: CentOS Stream 9 GNOME Version: 40.4 GPU Driver Version: 550.54.15 I would greatly appreciate any suggestions. Thanks, Wang GuangLei

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Discrepancy: plDDT laphafold3 and ChimeraX version 1.9.dev202405310031 (2024-05-31)
by Khawar Siddiqui 03 Sep '24

03 Sep '24

Dear Tom and ChimeraX team I recently did some protein structures using AF3. I found that the plDDT color prediction given by AF3 differs from when I opened the downloaded file in ChimeraX. Both photos are below. Can you please guide me to where I am making the mistake? Some adjustments may be needed. The AF3 coloring (right) shows prominently Blue-cyan (70-90% confidence) whereas after opening the same file in ChimeraX (left) shows many regions as yellow (50% confidence). Thanks again for the help. sohail Dr Khawar Sohail Siddiqui, [cid:3f847f24-9a1b-47bc-bb56-1704e8bd8ac3] [cid:2c952f1f-e76e-458e-a444-8242f6bdab3a] [cid:0089dce1-a9be-4009-93b9-d158c31cee29]hoo.com

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I found that the phosphodiester bond has broken.
by Yan ZHANG 张艳 03 Sep '24

03 Sep '24

Dear ChimeraX Team, I am writing this letter due to an issue I have encountered. I have adjusted the phosphodiester bonds of the RNA chain using Coot for structure correction. However, when I opened it in ChimeraX, it appears to be in a broken state, even though the distance between the two atoms is 1.6 angstroms. I am unsure what the reason for this could be. I have attached an image below. The dashed line should originally be a P-O bond. Could you please suggest any solutions to this problem? I look forward to receiving your reply as soon as possible. [cid:image001.png@01DAFDEC.77532DA0]

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Purchase license
by Lili Ye 03 Sep '24

03 Sep '24

Hello, I am from Sironax(Beijing)Co.,Ltd. We want to buy two licenses now, how to buy? Thanks! Lili Ye 叶丽丽 Sironax (Beijing) Co., Ltd. 维泰瑞隆（北京）生物科技有限公司 Add: Building 2, No.9 Yike Road, Zhong-Guan-Cun Life Science Park, Changping district, Beijing, China 102206 北京市昌平区生命科学园医科路9号院2号楼8层 Tel: （+86）15201581663 Email: Lili.Ye(a)sironax.com<mailto:Lili.Ye@sironax.com> [1534753277(1)]

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Inquiry About Building Molecular Structures in ChimeraX
by 化工化工 02 Sep '24

02 Sep '24

Dear Professor, I hope this message finds you well. I am currently engaged in machine learning research using ChimeraX. As part of my work, I need to substitute various groups on the phosphorus atom, including methyl, tert-butyl, cyano groups, and others. However, the current substitution function does not cover many groups, so I have been manually adding them to the SEQCROW library. At present, I am building the structures in Gaussian, which is quite cumbersome. Since I am not very familiar with ChimeraX, I am unsure whether it allows for manual molecular structure building. If such functionality is available, it would greatly assist my work. I would greatly appreciate any guidance or suggestions you might have. Thank you very much for your time and assistance. Best regards, Youcai Zhu 化工化工 1366924572(a)qq.com  

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Re: color bfactor by alphafold palette
by Elaine Meng 02 Sep '24

02 Sep '24

To summarize for users, the ChimeraX alphafold coloring to show pLDDT values is continuously shaded, whereas the coloring shown at the AlphaFold database is similar but discontinuous, and differences may be evident. The reasoning behind the ChimeraX alphafold coloring palette is that it may be more informative about the specific values. However, it may be confusing that it looks similar, yet not the same, as the AlphaFold database pLDDT coloring. A few months ago, Abnieszka Obarska (thank you!) helpfully provided a command to match the coloring shown at the AlphaFold database. Since it was in an image, however, it is not convenient for cut and paste, so I have copied it here: color bfactor palette 0,#FF7D45:50,#FF7D45:50.00001,#FFDB13:70,#FFDB13:70.00001,#65CBF3:90,#65CBF3:90.00001,#0053D6:100,#0053D6 Although I did not check if the color hex codes exactly match the AlphaFold database colors, I tried it on a couple of examples at least to my eye, it reproduced the coloring of structures shown at the database. 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

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AlphaFold PAE plot not generated
by Catrin McHugh 30 Aug '24

30 Aug '24

Good morning Having successfully generated a PAE plot (and coloured the model accordingly) with data generated by AF3, I am getting an error message when I try to do the same using a JSON file generated by ColabFold for AF2. The error message is: 'is not AlphaFold predicted aligned error data, expected a top level list". I attach the JSON file, and the relevant structure PDB. Many thanks in advance Catrin

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Random residue colors?
by Daniel Asarnow 30 Aug '24

30 Aug '24

Hi all, In the color command documentation, it says 'color random' can per atom or per residue. How can random residue colors be specified? I can only get random atom colors. Thanks! -da

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CIMERAX 64BIT FOR WIN 10
by Lee, Yong Sok (NIH/NIAID) [E] 29 Aug '24

29 Aug '24

I AM LOOKING A FOR A 64BIT VERSION OF CHIMERAX FOR WINDOWS 10. TRED DOWLOANDING AND INSTALLING CHIMERAX 1.8 BUT IT WOULD NOT LAUNCH ON MY WINDOWS 10 64 BIT SYSTEM. LET ME KNOW IF YOU HAVE A SOLUTION FOR THIS ISUUE. LOOKING FORWARD TO HEARING FROM YOU.

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Invitation to conduct a UCSF Chimera Workshop at Purdue University
by Ferdausi, Nourin 29 Aug '24

29 Aug '24

Dear Team, I hope this email finds you well. My name is Nourin Ferdausi and I am a graduate student at the Department of Biological Sciences in Purdue University. My colleague, Priyanka Naik (cc’d here) and I are writing to you on behalf of the Structural Biology and Biophysics Club (SBBC). We are hoping to organize a virtual workshop focused on UCSF Chimera, and we would be honored if one of your team members could conduct this workshop. The graduate students and researchers of our structural biology group use a wide variety of experimental approaches like cryo-electron microscopy and X-ray crystallography for determining molecular structures. Consequently, the Chimera software is integral to our research, and we believe your insights would be of great impact to our community. We are flexible with the format of this virtual workshop, which is tentatively scheduled for mid-September; however, we are open to adjusting the date based on your availability. Your participation will provide our members with a unique opportunity to learn directly from a developer of UCSF Chimera. Please let me know if we can have a quick Zoom call to discuss the event in detail. We look forward to your reply at your earliest convenience! Thank you, Nourin Ferdausi Ph.D. Candidate, Noinaj Lab Supporting officer, Structural Biology and Biophysics Club Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology West Lafayette, IN-47907-2054

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Re: [Chimera-users] Finding SASA for individual residues
by Elaine Meng 29 Aug '24

29 Aug '24

Hi Ale, In the future please use chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (CC'd here) for ChimeraX questions. This chimera-users@cgl address is for Chimera, which is a different program, and I don't want to confuse the other users. Everybody, this answer is for ChimeraX: I believe you are misunderstanding how "measure sasa" works. It will actually enclose the specified atoms in a surface, so if you say "measure sasa :12" that surface will only be around residue 12 and ignore all the other atoms. I am guessing that you really want the SASA of the aromatic rings in the context of the surface that goes around the whole protein, not for a bunch of individual bubbles drawn around each aromatic ring. In that case, your commands are wrong. Instead you want something like: measure sasa protein sum :trp,tyr,phe & aromatic-ring See "measure sasa" help for description of how it works: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> 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 Aug 29, 2024, at 4:16 AM, alessandro.strofaldi--- via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > I'll reply to this post for my question cause the title seems appropriate. > I've a one-chain protein and I simply want to calculate the SASA of the aromatic-ring of all TRP,TYR and PHE of the protein using ChimeraX. > > This is the log: > measure sasa /A > Solvent accessible area for /A = 22276 > measure sasa /A:trp & aromatic-ring > Solvent accessible area for /A:trp & aromatic-ring = 1824.9 > measure sasa /A:phe & aromatic-ring > Solvent accessible area for /A:phe & aromatic-ring = 3339.6 > measure sasa /A:tyr & aromatic-ring > Solvent accessible area for /A:tyr & aromatic-ring = 3977.3 > > But the I tried to get the sum: > > measure sasa /A:trp,tyr,phe & aromatic-ring sum :trp,tyr,phe > Solvent accessible area for /A:trp,tyr,phe & aromatic-ring = 7683.3 > Solvent accessible area for :trp,tyr,phe (285 atoms) of /A:trp,tyr,phe & aromatic-ring = 7683.3 > > Which is different from the sum of the values I got before. I think I'm missing something basic on SASA calculations... > Also, from your answer to Prathvi, those numbers should be squared Agstrom. Do these number make sense? For a single residue (measure sasa:263, which is a surface-exposed Tyrosine) I got 331.95. Those values are similar to what Prathvi got so am I doing the same mistake? I was expecting, for a single residue something like two order of magnitude less. > You said ".. then it will make a surface that only encloses that one residue, with area 292 as you said. I'm pretty sure that is NOT what you want. Instead you want tthe surface of the whole protein (or maybe one chain) and then the area of the residue given that larger surface. " Does this means that with the commands I typed ChimeraX "Isolates" the residue and calculate the SASA as if it was not included in the protein? > Anyway, I think it is clear I'm an unexpert user so If there is any tutorial about SASA on ChimeraX (could not find those, only for Chimera), please, feel free to suggest. > > Thank you!! > Best, > Ale

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