September 2024 - ChimeraX-users - RBVI Mailing Lists

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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Modelling of missed loop fragments in multi-chain structure
by Enrico Martinez 25 Sep '24

25 Sep '24

Dear Chimera-X users! I need to predict missed loop fragments in a part of a multi-chain complex corresponded to GPCR bound to heteromeric G-protein (pdb id 8HTI). In this structure the chain A (a subunit of the G-protein) contain missed loop fragments. So the following commands were executed in command line to reconstruct the entire structure of this subunit: open 8hti seq chain /A ui tool show "Model Loops" modeller refine 1/A:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard which very slowly produces 5 models of the chain A. The problem was that the modeller considered the chain A in isolation from the rest of the structure and predicted loops overlapped with other chains of the G protein. Would it be possible to reconstruct the missing fragments in the chain A considering also the presence of other chains to build the full complex ? Many thanks in advance Enrico

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Inquiry: Selecting Individual Electron Density Maps for Comparative Analysis
by Yan ZHANG 张艳 25 Sep '24

25 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 23 Sep '24

23 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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