August 2022 - ChimeraX-users - RBVI Mailing Lists

Find Residues From Specified Residue Numbers Help
by Myers, Jonathan 05 Aug '22

05 Aug '22

Dear ChimeraX Users, I'm learning how to use the Python API and I found the set of ChimeraX recipes and am trying to use the code featured on the "Find Residues From Specified Residue Numbers" page. I've run into the following issue: NameError: name 'structure' is not defined. I'm not sure what I should be using as an input for the "structure.residues" argument so I have not changed that input. What "structure" should I be specifying? Any help would be greatly appreciated. Shosholoza, Jonathan Myers

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Color by Chemical Shift Perturbations
by Nadun Chanaka Karunatilleke R Wasala Mudiyanselage Vihare 05 Aug '22

05 Aug '22

Hi admin, I am trying to color the protein surface based on the chemical shift perturbations. As mentioned in the example published on March 15th, 2021, I was able to color the surface. However, I needed to add 6 levels, and I failed to do so. It was possible to define the levels and colors in chimera but I failed to do so in chimerax. Is there a way to solve this? Thank you Nadun Nadun Karunatilleke Ph.D. Candidate Dr. James Choy's Lab Department of Biochemistry Schulich School of Medicine & Dentistry Western University London, Ontario, Canada N6A 5C1

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Use different distances for several marker sets
by SHIQING LIAO 04 Aug '22

04 Aug '22

Dear community, I'm wondering if there is any way for me to color a volume density with different distances from several marker sets. Thank you for your help! Best, Shiqing

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Time-efficient python code for obtaining coordinates of atoms
by Shubham Devesh Ramgoolam 03 Aug '22

03 Aug '22

Hi all, I hope you are doing well. I am looking for a time-efficient way of obtaining the coordinates of specified residues. I cannot use the command getcrd as I need these coordinates in a python script for defining geometric objects (getcrd prints the output to the log). My attempt at this consisted of selecting all of the specified residues via run(session, ‘sel ...’), accessing that selection using selected_residues(session), and then, extracting the coordinates using .atoms.coords. The issue here is that run(session, ‘sel ...’) slows down if there are lots of specified residues. I tried bypassing the command ‘sel’ by first importing AtomSpecArg from chimerax.core.commands.atomspec and then using AtomSpecArg.parse('my residue_ID', session)[0].evaluate(session).atoms[0]. However, this is even slower. Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Error message
by Kwangjun Lee 02 Aug '22

02 Aug '22

Hello, I was trying to find residues within the dimerization interface. I have watched the video https://www.youtube.com/watch?v=TMcjEecFHaI&t=17s [https://i.ytimg.com/vi/TMcjEecFHaI/maxresdefault.jpg]<https://www.youtube.com/watch?v=TMcjEecFHaI&t=17s> Evaluating AlphaFold protein-protein binding with ChimeraX<https://www.youtube.com/watch?v=TMcjEecFHaI&t=17s> We show how to display AlphaFold predicted aligned error for residues at the binding interface between two proteins, encapsulin and ferritin, using ChimeraX.... www.youtube.com and follow the instructions but I got an error message and it seems others have the same issue with me. Is it a bug or did I do something wrong?? Thanks! Kwangjun Lee Ph.D. Candidate Department of Biomedical Sciences Florida State University College of Medicine 1115 W. Call Street Tallahassee, FL 32306 Tel: (850) 491-6985 Email: kwangjun.lee(a)med.fsu.edu<mailto:hyojeong.yong@med.fsu.edu>

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ChimeraX change chain IDs tool not available
by Rish, Anthony 02 Aug '22

02 Aug '22

Hello, I created a protein model with 9 separate chains and fit it to my experimental cryo-EM map. However, once I saved the new model, relative to the map, the chains were renamed to 1.1/A, 1.2/A… 1.9/A. This is no good since all chains now are labeled as A in the PDB file and programs like PyMol can’t tell the difference between the chains. I checked the ChimeraX user guide and there is supposed to be a tool for this exact problem called change chain IDs under the Tools->Structure Editing tabs, using the command changechains, but the tool is nowhere to be found. I’m running the current build of ChimeraX as of 8/2/22. How can I change the chain IDs of my model? Thanks, Anthony

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Sorting the required molecules in cvc file
by Dmitry Semchonok 02 Aug '22

02 Aug '22

Dear colleagues, I would like to find out about the possibilities. I have a model that contains apart from the other data, the pigment molecules – chlorophylls, carotenoids etc. Is there a way sort certain types of molecules in a *.cvc file by chimeraX so that the following information will be shown? Mol,Label,Element,X,Y,Z CHL,n 606,NC,267.342,151.989,253.363 CHL,n 606,MG,266.202,151.941,255.073 CHL,n 607,NB,275.512,153.952,252.428 CLA,n 610,MG,273.005,139.807,270.918 CLA,n 611,NB,288.916,127.885,266.725 Thank you! Kind regards, Dmitry

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Superposing protein structures
by Alicia Gardiol 01 Aug '22

01 Aug '22

We have experimental protein structures in PDB, and Alpha Fold predicted structures. Which is the best software to superpose these structures using a MAC computer. - Two different predicted proteins (predicted 1 to predicted 2) and - Same protein predicted and experimental (predicted 1 to experimental 1) Thank you and best wishes. Alicia Gardiol, PhD

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Re: [chimerax-users] Model panel for multi-state objects of dimeric protein
by Elaine Meng 01 Aug '22

01 Aug '22

Hi Enrico, I haven't figured out why this doesn't work on your example (omitted since mailing to the list): close #1 & ~ #1.5 However, this works: delete #1 & ~ #1.5 Also if you didn't have other models (#2 etc.) that you were trying to keep you could just use delete ~#1.5 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 1, 2022, at 6:39 AM, Enrico Martinez <jmsstarlight(a)gmail.com> wrote: > > Hello Elaine, > I just faced the same problem that has been indicated in this topic > Thi time I am dealing with the monomeric multi-model complex obtained > from docking. > Here is the example of a pdb file consisted of 80+ docking poses. To > keep only the 1.5 sub-modeli've tried to use > close #1 & ~ #1.5 > but this produced nothing, while for other pdbs it works fine. Could > you tell me what's wrong with it? > Many thanks in advance > Cheers > Enrico

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Reduce figure size for export for publication
by Fossati, Andrea 01 Aug '22

01 Aug '22

Hi, How to best export figure at high-ish resolution to then add it to an already made illustrator panel? After some googling seems vector-based export is not possible so what is the recommended format and which resolution is best for 3x3 inch illustrator panel? At the moment I am exporting as TIFF with transparent background and size 5000 and supersampled 4 times to keep high res but the file has like 15Mb per structure which is not feasible/handy to modify. What is the suggested solution for paper figures? Best, Andrea Fossati, Ph.D Krogan Lab

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ChimeraX-users August 2022