October 2025 - ChimeraX-users - RBVI Mailing Lists

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

2 1

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... >

2 5

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

2 2

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

2 1

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

2 2

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>

2 4

Issue with the coordset slider in chimeraX
by jeandidier.marechal＠uab.cat 05 Oct '25

05 Oct '25

Hi everyone, I am starting to take steps into ChimeraX handlers of MD simulations. So far, there have been no problems loading the starting PDB file and the trajectory. However, I am unable to make the coordset slider work. I always have the minimal version with the frame slider, the snail, and the recording button. Nothing happens when running the coordset slide #number_of_the_model. So, I can not make distance plotting and so on. I tried different versions of the software, including the latest daily build and the most recent production release. Thanks a lot for telling me what I do wrong and, if not readily implemented, please apologize for my impatience ;-) Cheers JD

2 1

Struggling to complete assignment at last minute? Hire our Assignment helper
by mglen142＠gmail.com 04 Oct '25

04 Oct '25

Being a student, you may juggle several things in academics. Students are burdened with several academic tasks. Managing lectures, self-study, homework, exams, tests, and academic projects at the same time can be difficult for students. Sometimes students forget the deadline and seek urgent help for the academic assignment. Seeking last-minute writing assistance, you can connect with our <b><a href="https://us.assignmenthelppro.com">Assignment Helper</a></b> in the USA. They can help you to complete the assignment timely and excellently. The experts are trained to work fast on academic assignments. Professional experts are ready to assist students at any time with any type of writing need. With their support, you can complete the assignment on time and meet the urgent deadline. Their support allows students to manage busy schedules and focus on learning other necessary things or mastering the subject.

1 0

Save centroids in scene coordinates
by Andrew Kennard 03 Oct '25

03 Oct '25

Hi there, I have aligned a bunch of models with matchmaker, and then I defined centroids for each model with `define centroid`. I would like to export those centroids for further analysis (trying to see the spatial relationship between chains B from each model when all models are aligned on chain A). However, the only way I could figure out how to do it was to press "Save Info..." in the Structure Measurements window. This text file reports the centroids in the model coordinate system for each model. But because I aligned the models with matchmaker, I'd rather have the centroids in the scene coordinate system. I am not sure how to do this transformation and export all the coordinates (~dozens of models). The only other option I found that might work was the `getcrg` command which I could use to save the coordinates to the Log, but then I will have to save the log as an HTML and parse that, right? Is there any more straightforward way? Alternatively, is there a better way to define centroids (ideally programmatically) so I can extract them from Chimera easily in scene coordinates? Perhaps the measure center command is the thing I should be using? Thanks a bunch! I'm running ChimeraX v1.10.1 (2025-07-24) on Mac OS 15.6 Sequoia Thank you!! Andrew

2 3

de novo octahedral assembly of AlphaFold-generated ferritin monomers
by jmcquaid＠ucsd.edu 03 Oct '25

03 Oct '25

Hi folks! I would like to use "Sym # O" to model how a novel marine ferritin might assemble into an octahedral nanocage. Like ferritin, this marine ferritin is thermostable and has a size consistent with a 24-mer, but the AA sequence is too divergent to use 'matchmaker'. I've noticed that if I create a fold model of human ferritin (1FHA) with AlphaFold and import it into ChimeraX, the 'sym # O' command generates a 24-mer hairball rather than an octahedrally-coordinated sphere. If I 'fetch' the same 1FHA protein directly from PDB, the spherical structure is correctly assembled. What additional commands might be needed to help ChimeraX correctly assemble an AlphaFold-generated 1FHA monomer into the canonical ferritin cage? Chimera used to have a 'group 432' command, but I see this is not currently supported. Thanks in advance! Knowing how to correctly assemble something known like human ferritin will greatly help in assembling something unknown like a marine ferritin. Best Regards, Jeff McQuaid, Scripps Institution of Oceanography

3 4