- 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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