- ChimeraX-users - RBVI Mailing Lists

Re: [Chimera] local resolution map colors
by Elaine Meng 03 Oct '25

03 Oct '25

Hi, This question was sent to the commercial licensing address -- for user questions, please use the email address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here to ensure that you get an answer instead of mystified silence. Is the local resolution map open in addition to the original map? I only see two copies of the same map in the Volume Viewer. Make sure that you open the local resolution map instead of a second copy of the original map. 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 Oct 3, 2025, at 2:07 PM, Roy Chowdhury, Shatabdi wrote: > Hi, > > In the past, I've used chimerax to display local resolution on maps using the tools->volume data->surface color function. In a new map, I'm having difficulty with it. I'm attaching screenshots where the phenix local resolution job suggests the resolution range to be 1.27A - 4.6A range which is in agreement with cryosparc. When I load the cctbx_program.ccp4 file on chimerax, it is unable to color the surface and says the surface values are -0.067 - 0.107. Is there something I should be doing differently? Any suggestions would be deeply appreciated. > > Thanks! > > Shatabdi Roy-Chowdhury, PhD. > Cardiovascular Research Institute > University of California, San Francisco > > _______________________________________________ > Chimera mailing list -- chimera(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-leave(a)cgl.ucsf.edu

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Defining pdb chain ontologies
by Pranav Shah 30 Sep '25

30 Sep '25

Hi Team, I am writing to inquire about the functionality of ChimeraX, specifically concerning multi-subunit complexes with multiple chains of a single protein (e.g., PDB 4v7q). I am wondering if there is a feature that allows for manipulating chains by assigning them to functional ontologies. For instance, with the 4v7q example, I would like to be able to execute commands such as: color #1 "vp4" red `mm #1/"vp4" to #2/"vp4" These ontologies could be grabbed from the cif file and if the user decides define their pwn ontologies/groupings. If such a feature does not exist, would you consider exposing such a feature to the user? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Orient many tetramers
by Alexandra Zahradnikova 30 Sep '25

30 Sep '25

Hi I have a set of tetramers created by AlphaFold. They are randomly oriented. In order to measure their pore size in a third-party program, I need to orient them with their z axis pointing in the z direction. I can orient them with respect to the screen, but I don't know how to save this view orientation (i.e. so that the z axis in the pdb file goes vertically). Is there any way how to do it? The switch in the "save" command specifying whether to use transformed or untransformed coordinates does not make any difference, and the file is always saved in the original orientation. Best Sasha

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Suggestion for viewdock
by John Irwin 29 Sep '25

29 Sep '25

Hi Team We love viewdock. We would like to suggest allowing hotkeys for adjusting status e.g. for prioritization so that we do not need to mouse all the way down to click to change status. We think this might be a small change with a big usability and productivity impact. Thank you John John Irwin UCSF Pharmaceutical Chemistry http://irwinlab.compbio.ucsf.edu

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Just a Big Thank You
by Esmaeeli,Reza 25 Sep '25

25 Sep '25

Dear ChimeraX Developers, This is Reza and I’m a computational chemist and protein designer. I’ve been a long time user of Chimera and now ChimeraX. Among many visualization programs that I have tried extensively including PyMOL, VMD, Maestro, ChimeraX has remained my favorite. I just wanted to take a moment and write this email just to say thank you for your amazing work. Even though it is free for academic users, this email is the least I should do after so many hours that I have enjoyed using it. The interface is great. The diverse set of features and modules are awesome. And the command line and scripting capabilities are so intuitive and easy to use. Can’t wait to see what comes next. Best Regards, Reza ChimeraX 1.10.1 on macOS Tahoe

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Re: [Chimera-users] Mapping conservation onto a structure
by Elaine Meng 25 Sep '25

25 Sep '25

Hi Shelley! Chimera and ChimeraX are two separate programs, so there are various differences. The email address for ChimeraX questions, chimerax-users(a)cgl.ucsf.edu is CC'd here. I'll answer for ChimeraX since that's what you're using -- ChimeraX has a Sequence Viewer tool which is basically the logical equivalent of Chimera's Multalign Viewer, see: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> See also the detailed tutorial on using ChimeraX to map conservation from a sequence alignment onto structures: <https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-…> 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 25, 2025, at 8:36 AM, Shelley Copley via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Has Multalign viewer been taken down? I don’t see it in ChimeraX 1.10. Is there a different way to map sequence conservation onto a structure? > Thanks! > Shelley

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Is there a way to download a pdb and it's associated density map in one command
by Samuel Haysom 24 Sep '25

24 Sep '25

Is there any way I can fetch a pdb file from the web (e.g. $ open 1X2Y) and then also automatically fetch the associated cryoEM map if there is one? Looking in the mmCif file, there is a flag for the associated emdb-map (e.g. in 5ljo the mmCIF file there is a _pdbx_database_related.db_id flag with the corresponding id. It would be useful if this could be added as a flag to the open command if it isn't already. I'm sure it is also possible in some kind of script but I'm not hugely familiar with how to script in chimeraX. Samuel Haysom Senior Scientist • Protein Sciences Nxera Pharma UK Limited +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

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Ligand center
by NUR AIDA SAKINAH 24 Sep '25

24 Sep '25

Hi ChimeraX teams, I want to search ligand center for docking analysis. What command do I need to use to retrieve the ligand center (x,y,z)? Example pdbid is 4yvv and the ligand is GBM. So i want the GBM's x,y,z coordinates. Thank you. Regards, Aida.

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Regarding the method used by chimeraX for SASA calculation
by Prathvi Singh 23 Sep '25

23 Sep '25

Hi Elaine, I have used NACCESS ( https://www.bioinf.manchester.ac.uk/naccess/nac_intro.html) to calculate the SASA for a protein. It used the Lee & Richards (1971, J. Mol. Biol., 55, 379-400) method to calculate SASA. I wanted to know whether chimeraX also uses the same method to calculate SASA or not. If not, then can you mention how the chimeraX method differs from the method used by NACCESS? Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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About "Minimizing Structure" feature in Chimera
by Zheyun Wang (MED,124090655) 23 Sep '25

23 Sep '25

Dear ChimeraX developers: I am Wang Zheyun, a student in Chinese University of Hong Kong, Shenzhen. In my computational biology course, our professor demonstrated to us that the molecular structure (a file containing several water molecules) can be changed to an energy-minimizing structure using "Minimizing structure" function in Chimera. However, I cannot find this function in ChimeraX(1.10.1), and professor told me that these two are completely different softwares. Is this function available in ChimeraX? If so, may I know where it is? If not, will this be added to ChimeraX or is it deliberately deleted? Looking forward to your reply! Sincerely, Wang Zheyun

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