August 2025 - ChimeraX-users - RBVI Mailing Lists

Residue Interaction Network visualisation using chimerax
by Gagandeep Singh 20 Aug '25

20 Aug '25

Dear team , I have generated residue interaction network (RIN) data using RING 4.0 and would like to visualize this . I am familiar with UCSF Chimera, which supports visualization of RIN data, and I was wondering if ChimeraX also offers similar functionality. Kind regards -- *गगनदीप सिंह **/ Gagandeep Singh* *डॉक्टरेट का विद्यार्थी **/ Doctoral student* *ब्रिक - ट्रासलेशनल स्वास्थ्य विज्ञान और प्रौद्योगिकी संस्थान* *BRIC- Translational Health Science and Technology Institute* *(भारत सरकार के जैव-प्रौद्योगिकी विभाग का एक स्वायत्त संस्थान)* *(An autonomous institute of the Dept of Biotechnology, Govt Of India)* *NCR Biotech Science Cluster,* *3rd Milestone, Faridabad–Gurugram Expressway,* *PO box #04, Faridabad- 121001 (Haryana)*

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Question about the software features
by Mazrouee, Sepideh (NIH/OD) [E] 19 Aug '25

19 Aug '25

Hi, I had the chance to use ChimeraX recently for aligning some predicted protein 3D structures and it looks wonderful. However, I need to do some labeling of the visualization (including labeling of specific protein domains) and I wasn't sure if such feature exists in the software or there might be a way to make it happen. I would highly appreciate your help if you could provide me with some online resources to educate myself or join a call with some team members to help us out. Best regards, Sepid Sepideh Mazrouee, PhD Researcher, Office of Data Science Strategy (ODSS) Office of Director, National Institute of Health (NIH<https://www.nih.gov/>)

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Select atoms/chains by _atom_site.label_asym_id instead of _atom_site.auth_asym_id?
by Ute Roehrig 19 Aug '25

19 Aug '25

Hello, Is there a way to select atoms/chains from a mmcif file by their _atom_site.label_asym_id value instead of the _atom_site.auth_asym_id value? Thank you for your help, Ute

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Question Regarding Contacts Command in ChimeraX
by Andrew Guo 19 Aug '25

19 Aug '25

Hello, My name is Andrew Guo, an undergraduate at the University of Maryland College Park, doing research under Dr. John Orban with help from Dr. Andy LiWang from the University of California Merced, in the field of protein fold switching. Dr. LiWang recently used ChimeraX to calculate vdW contacts closer than 3.8 A between carbons in the context of a fold switching region in a small list of 26 "metamorphic" proteins (see here <https://doi.org/10.1073/pnas.2422725122>). I am now working on automating the whole process of calculating these contacts. In doing so, I have encountered a strange inconsistency that I do not know how to fix, and was hoping to gain some insight from the people who have developed ChimeraX. Previously, the overall contacts count was calculated by first calculating interdomain contacts then intradomain contacts and summing the two. It would be much simpler to calculate the contacts in one "whole" command instead of restricting the command to just interdomain or intradomain contacts. However, I have found that this "whole" command sometimes includes ligand contacts. For instance, for the pdb code 4O01A and region of interest residues 446-478, I have the following set of commands: interdomain: contacts /A:446-478@C* restrict /A:1-445,479-506@C* distance 3.8 reveal true name vdW output 13 intradomain: contacts /A:446-478@C* restrict /A:446-478@C* distance 3.8 reveal true name vdW output 8 "whole": contacts /A:446-478@C* restrict /A@C* distance 3.8 reveal true name vdW output 22 Obviously, 13 and 8 do not sum to 22. Ligand command: contacts /A:446-478@C* restrict ligand distance 3.8 reveal true name vdW This ligand command had an output of 1 and was the following: /A LEU 463 CD1 /A LBV 600 CMA (alt loc A) This contact was also the extra contact found in my "whole" command output, so I could just run the two commands (whole and ligand) and subtract the output of the ligand command from the output of the whole command. However, for the pdb code 3KMZA and region of interest residues 393-421, I have the following: interdomain: contacts /A:393-421@C* restrict /A:1-392@C* distance 3.8 reveal true name vdW output 0 intradomain: contacts /A:393-421@C* restrict /A:393-421@C* distance 3.8 reveal true name vdW output: 1 distances atom1 atom2 distance /A MET 400 CG /A GLU 401 C 3.788 "whole": contacts /A:393-421@C* restrict /A@C* distance 3.8 reveal true name vdW output: 1 distances atom1 atom2 distance /A MET 400 CG /A GLU 401 C 3.788 ligand: contacts /A:393-421@C* restrict ligand distance 3.8 reveal true name vdW output 6 1-6 = -5 contacts Using my method, I get -5. Clearly, this is bad. The ligand command gave these 6 contacts: 6 distances atom1 atom2 distance /A THR 397 CG2 /A GOL 3 O3 3.321 /A ARG 394 CD /A GOL 3 O2 3.411 /A ILE 396 CA /A GOL 3 O3 3.436 /A ILE 396 CG2 /A GOL 3 O2 3.667 /A ILE 396 C /A GOL 3 O3 3.703 /A ILE 396 CB /A GOL 3 O3 3.721 However, these contacts were not part of the output of the whole command, unlike in the case of 4O01A. Is there something I am doing wrong with how I am setting up my commands? Please let me know if further information is needed! Thank you, Andrew

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Log Setting
by NUR AIDA SAKINAH 18 Aug '25

18 Aug '25

Hi ChimeraX teams, I am using ChimeraX version 1.9 in dark theme, when open the saved session, the log shown in highlighted grey colour if i’m not mistaken. So, is there a setting to make it easier to view the log for the saved session? Thank you. Regards, Aida

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B-factor and error in distance measurements
by Charles Midgett 18 Aug '25

18 Aug '25

I have two structures of a protein solved to different resolutions, one pretty good and the second not so good, and I want to compare distances between congruent atoms in the structures. It occurred to me that I have no idea if the differences in the distances are within the positional error of the atoms or not. Therefore, is there a way to propagate the positional uncertainty in the B-factors into a linear distance uncertainty? Sincerely, Charles

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Multiple sequence alignment display
by Betancurt, Leonardo 18 Aug '25

18 Aug '25

Hello, I would like to display a multiple sequence alignment based on structure after match maker. I use the command ”mm #!1-4 to #5 showAlignment true” but ChimeraX shows multiple pairwise alignments, is there a way to create a multiple sequence alignment? Thank you, Leo Betancurt, Ph.D. Post Doctoral Researcher | Zatopek Lab<https://www.neb.com/en-us/research-labs/zatopek-lab?srsltid=AfmBOoqPDIvrCfa…> New England Biolabs Inc. 📞 (978) 380-7290 📱 (351) 350-4075 [signature_474729057]<http://www.neb.com/>

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Re: ChimeraX support: Alphafold contacts
by Elaine Meng 14 Aug '25

14 Aug '25

Hi Tony! There are lots of options in menu: Select... Contacts, so it rather depends on all of the specific settings that you chose. Here is the help for that GUI: <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> To summarize in regard to your questions... If you are in the Chains tab, you have a choice to use atomic distance or buried surface area. If you chose atomic distance it is using all the atoms and doesn't care what is backbone or sidechain. It would be the minimum distance (closest pair). At any point you can just simply list the residues in the current selection, e.g. command info residues sel ... which will go to the Log but you could alternatively save to file, e.g. info residue sel saveFile ~/Desktop/contacts.txt If you are in the Atomic tab, then you have the choice to use VDW overlap (negative distance between VDW surfaces) or center-center distance as the main criterion. If using that tab, presumably you would have already selected one of the chains and then designate to limit the results to atom pairs where one of the atoms is selected. You don't have to go through GUIs. If you just want to list residues in one chain with any atom within some distance of any atom in another chain, you could use commands like the following to select protein residues in chain A within 5.0 Angstroms of protein residues in chain C. The "protein" intersections are because some structures have water, ligand, ions with the same chain IDs as the protein chains, but I wanted to only consider the protein. select (/A & protein) & (/C & protein) :<5.0 info residues sel If the chains were only protein anyway, or you wanted to include any nonprotein residues, could be simpler select /A & /C :<5.0 See command-line zone specification and combinations such as intersection (&): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones> Again it is all atoms and the closest pair. 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 10, 2025, at 5:39 PM, Anthony Newcombe <anthony.newcombe(a)appliedbiopharm.com> wrote: > > Hello Elaine > > I have a commercial license of ChimeraX. Further to the email below, I have been using the menu and GUIs to select > contacts as described in your online message below > > https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… > > This highlights the residues, and returns ' 267 atoms, 264 bonds, 32 residues, 1 model selected' between chains A and C > > But is there a simple command to list the identified residues as an output that are within less than 5 Angstroms and may interact for chain A or chain C, ie > > LEU264 > SER265 > ALA266 > > Also one question regarding the atomic distance used, is this a max distance between side chains, or the distance between the peptide backbones? > > Thanks for the help and apologies if these are simple questions > > Many thanks > > Tony

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Assistance: ChimeraX morph
by Priyanka Abeyrathne 12 Aug '25

12 Aug '25

Hi, I have two cryo-EM models (PDBs) at neutral and acidic pH conditions, both containing 486 amino acids. I would like to compare them by calculating the RMSD per residue, and then generate a morphing animation between the two structures. I used the following commands in ChimeraX: 1. I aligned the two structures using MatchMaker: mm #1 to #2 showAlignment true 2. I clicked on one amino acid in the MatchMaker alignment results to highlight the aligned residues. 3. Then I used the command: select ~sel to select residues with an RMSD greater than 1 Å. 4. To visualize the atoms of the selected residues with high RMSD, I ran: display sel & protein 5. I then cleared the selection using: select clear 6. Finally, I attempted to generate a morphing animation using: morph #1,2 wrap true frames 60 However, this command did not work. Could you please help me troubleshoot this? Thank you. Kind regards, Priyanka

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Creating an AtomicStructure object (along with other atomic objects) from scratch using Python API
by nrajan53045＠utexas.edu 11 Aug '25

11 Aug '25

Hi there, I am new to ChimeraX and its python API. As I was looking through the documentation, I noticed there were some atomic data classes (AtomicStructure, Atom, Atoms, Residue). Say I have a PDB file with information about all the atoms in the model, am I able to simply create Atom objects from reading the PDB file and, consequently, add these Atom objects to an AtomicStructure object? The reason I want to do this is because I want to use the fitmap function while limiting any disk IO. So, opening the file in ChimeraX (even if using the no gui offscreen functionality) would not work. I thought of simply creating objects from scratch, but I am running into errors when instantiating them. Sorry if this is an obscure problem or if I was unclear. Thanks for your help! Best, Nikhil

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