- ChimeraX-users - RBVI Mailing Lists

help on color command
by James Raymond 12 Oct '25

12 Oct '25

Dear ChimeraX, I have tried 100 variations of color command without success. Can you tell me the command to color residues 132-145 red in this single chain protein? thank you Jim [image: image.png]

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Issue with combining two pdb models in chimeraX
by Rayees Mattoo 10 Oct '25

10 Oct '25

Hi, I have two models #1 Model1.pdb and #2 Model2.pdb having one shared polypeptide, same chain ID but different residue numbers. I wanted to combine them to make a merged_model #3. I used the following combine commandline in chimeraX: combine #1 #2 close false modelId #3 retainIds true name merged_model The resulting combined model appeared to be correct, and I proceeded to run phenix.real_space_refine without any issues. However, when I attempted to deposit the refined model (either in .pdb or .cif format) with the wwPDB, I received a file with multiple errors (see attached). Interestingly, I had previously deposited the individual models (#1 and #2) without any problems. This situation raises my concern about whether the combination process was successful. Is there anything I should have done differently to ensure a seamless combination of the models? Best Rayees

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ChimeraX-1.10.1 syntax issue
by wwvivian.wang＠mail.utoronto.ca 10 Oct '25

10 Oct '25

Hi, this is my first time using ChimeraX-1.10.1 and I ran into a little bit of trouble with syntax errors in this version.\ I opened a pdb file that contains two chains of proteins that I'm interested in - Chain A and B. I then renamed and coloured them to Chain C and D for clarity. In the Contacts window, I made the following changes: Find pairs of atoms with: ✅ VDW overlap ≥ –0.4 Å Limit by selection: ✅ with at least one end selected Ignore interactions between atoms 4 or fewer bonds apart: ✅ Ignore interactions between residues <5 apart: ✅ Include intermodel: ✅ Include intramodel: ❌ (uncheck it) Include intramolecule: ❌ (uncheck it) Ignore hidden models: ✅ Display as pseudobonds: ✅ (keep green, radius 0.075, dashes 6) Write info to: Log ✅ Then click Apply I then selected the atomic model #1 (Chain C+D) and deselected surface models #1.1 (Chain C) and #1.2 (Chain D) and ran the Contacts Command: "contacts atoms #1/C #1/D makePseudobonds true distanceCutoff 4.0 log true" but the software returns "Expected a keyword" argument and highlighted "distanceCutoff 4.0 log true" in red. Alternatively, I also tried "findclash #1/C test #1/D overlapCutoff -0.4 hbondAllowance 0 interModel true intraMol false intraRes false makePseudobonds true select true log true" but again it fails to output contact coordinates between the two chains and returns the following: "Unknown command: findclash #1/C test #1/D overlapCutoff -0.4 hbondAllowance 0 interModel true intraMol false intraRes false makePseudobonds true select true log true". I would appreciate your help in resolving this error for me. Thanks, Vivian

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Focus in ChimeraX
by Luca Pellegrini 10 Oct '25

10 Oct '25

Hi, What is the ChimeraX equivalent to the Focus command in Chimera? I have selected a portion of a structure, and would like to bring it into focus without dragging it into view. Also Focus would automatically set the selection as the pivot point. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA lp212(a)cam.ac.uk

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Question about using ChimeraX
by 张圃源 09 Oct '25

09 Oct '25

Hi， I'm a new user of ChimeraX and I'm currently facing a problem. I want to convert a pdb file into an mrc file that can be input into cryoSPARC, and this mrc file should be in the form of a cube volume. I will use ChimeraX to achieve this. How should I proceed? Best Yuan 中山大学张圃源

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tools for ligand-receptor interactions
by Elaine Meng 09 Oct '25

09 Oct '25

> On Oct 8, 2025, at 9:58 AM, Vojo P Deretic <VDeretic(a)salud.unm.edu> wrote: > > Hi > How do I pose a question - via email or on the site? > My question is: we have a Boltz/alphafold fitted organic molecule into a known structure. > What are the tools for residue interactions in ChimeraX apart from H bonding and hydrophobic or charged surfaces? > Thanks > Vojo Deretic > Hi Vojo, As per the Contact Us page <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html> ...to ask questions you would use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address, which is CC'd here so you don't need to send your questions again. I don't know what you mean by "on the site" since there is no webform for questions, only this email address. You already mentioned H-Bonds and coloring the receptor molecular surface by ESP (electrostatics) or MLP (lipophilicity). That's most of it. Certainly you can just visually evaluate what is nearby, but you could use the Contacts tool for a more objective approach: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> See also the tutorial "Protein-Ligand Binding Sites" <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> 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 8, 2025, at 9:58 AM, Vojo P Deretic <VDeretic(a)salud.unm.edu> wrote: > > Hi > How do I pose a question - via email or on the site? > My question is: we have a Boltz/alphafold fitted organic molecule into a known structure. > What are the tools for residue interactions in ChimeraX apart from H bonding and hydrophobic or charged surfaces? > Thanks > Vojo Deretic > > Sent from my iPhone with lots of typos and autocorrect nonsense - my apologies... >

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Append ligand coordinates from one PDB to another
by George Tzotzos 08 Oct '25

08 Oct '25

I’m dealing with two structurally similar proteins, one of which is in complex with a ligand (pdb1). The second protein is in the apo-form (pdb2). I’ve used matchmaker to superimpose the structures. Does it make sense to append the ligand coordinates to pdb2? I’m interested to find out which residues lie within 4-5 Å from the ligand. Probably a better approach would be to dock the ligand to pdb2. Could this be done through ChimeraX using Boltz2? Thank you for your suggestions. George

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Issue in displaying pdb in chimeraX
by Rayees Mattoo 07 Oct '25

07 Oct '25

Hi, I merged two molecules in coot and generated a merged.pdb file. However, upon displaying in ChimeraX part of my model is cartoon and part of it displays as worm, see the attachment. After running dssp I can fix it, but I want it to display as cartoon by default. Anything I need to edit in the merged.pdb file? Best Rayees

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Modeller interface
by Alexandra Zahradnikova 07 Oct '25

07 Oct '25

Hi All, Today I am getting problems when trying to model loops with Modeller. Repeatedly (on different structures), the following error occurs: modeller refine 1/A:1:internal-missing numModels 1 fast false adjacentFlexible 1 protocol standardException in thread Thread-33 (_run_function): Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.10\bin\Lib\threading.py", line 1038, in _bootstrap_inner self.run() File "C:\Program Files\ChimeraX 1.10\bin\Lib\threading.py", line 975, in run self._target(*self._args, **self._kwargs) File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-packages\chimerax\core\tasks.py", line 300, in _run_function func(*args, **kw) File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-packages\chimerax\webservices\cxservices_job.py", line 156, in run reason = json.loads(e.body)["description"] ^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10\bin\Lib\json\__init__.py", line 346, in loads return _default_decoder.decode(s) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10\bin\Lib\json\decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10\bin\Lib\json\decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0). Is it a problem with the Modeler server? How can I find out in the future whether there is a problem with the server or the problem is in my input structure? Thanks in advance. Best regards Sasha

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Re: [Chimera] local resolution map colors
by Elaine Meng 06 Oct '25

06 Oct '25

I can't tell anything from the image, since I have no idea what your filenames mean. All I can say (again) is you have to open both the original map and the local resolution map, show the original map as a surface, and use the local resolution map values to color that surface. Elaine > On Oct 3, 2025, at 2:32 PM, Roy Chowdhury, Shatabdi <Shatabdi.RoyChowdhury(a)ucsf.edu> wrote: > > Hi Elaine, > > Thanks for your reply. Attaching the new screenshot here. This shows that the map values are 0.1095 all over. Please let me know if I can give any additional information. > ~Shatabdi > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Friday, October 3, 2025 2:20 PM > To: Roy Chowdhury, Shatabdi <Shatabdi.RoyChowdhury(a)ucsf.edu> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera] local resolution map colors > !-------------------------------------------------------------------| > This Message Is From an External Sender > This message came from outside your organization. > |-------------------------------------------------------------------! > > 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 > > > <Screenshot from 2025-10-03 13-56-32.png><Screenshot from 2025-10-03 13-56-51.png>> _______________________________________________ > > Chimera mailing list -- chimera(a)cgl.ucsf.edu > > To unsubscribe send an email to chimera-leave(a)cgl.ucsf.edu > > > <Screenshot from 2025-10-03 14-29-30.png>

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