March 2022 - ChimeraX-users - RBVI Mailing Lists

Chimera and ChimeraX commercial license
by Jai Vekeria 15 Mar '22

15 Mar '22

Hello, My name is Jai, I am a data scientist at Tectonic Therapeutics in Watertown MA, I would like to purchase 5 commercial licenses for Chimera and ChimeraX, I am assuming based on the little technical information included on the product page, that any windows 10 64-bit machine would suffice, we have some machine with a 1 Gb of ram and a 1.2Ghz processor and no GPU that we plan to use. Thanks, Jai Disclaimer The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful. This email has been scanned for viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business. Providing a safer and more useful place for your human generated data. Specializing in; Security, archiving and compliance. To find out more visit the Mimecast website.

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Outputting ChimeraX RMSD values after using matchmaker in a .PY script?
by Steven Truong 14 Mar '22

14 Mar '22

Dear ChimeraX admins, I am using matchmaker (mmaker) since the RMSD calculations done using the function have been very useful. However, I’m currently having some trouble outputting these values. At first, I tried to use matchmaker in a .PY script and then output these values via “log save”. Unfortunately, I haven’t been able to get this to work because whenever I try to do “log save” in a script (in terminal/command line), I get “no log tool to save”. Is there a way to “log save” if running a .PY script in a command line? Or is there a simpler way to get the values I need from matchmaker? Thank you for your help, Steven Truong sdt45(a)cam.ac.uk<mailto:sdt45@cam.ac.uk>

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solvate
by Joe Greenstone 13 Mar '22

13 Mar '22

In Chimera, solvation can be done via Tools/Structure Editing/Solvate How is solvation done in ChimeraX ? Thanks in advance.

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Aligning small molecules, ligands
by Noriega, Heather 12 Mar '22

12 Mar '22

Hello, I hope you are well Elaine. I am wondering if there is a way to align my combined model UNL to my model 2. In hopes this could be a reference model of my docking done in Chimera for future builds. I did figure out the bonding, thank you. :) I attached the session, and have read the align command. I am just unsure how to manipulate it to superimpose the ligand. align matchatoms (the whole model 2) toAtoms (UNL on model 1). Thanks for your help. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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2D Residue Plot
by Avinoam Aryeh Singer 11 Mar '22

11 Mar '22

Hey there, I was wondering whether there was a way to control the angle of the 2D residue plot generated from the "Interfaces" tool, such that creating plots from two aligned proteins will give me comparable plots. As you can see in the image below, the two structures are slightly rotated relative to one another, despite being aligned. Thanks! Avi Singer ?[cid:05b972a6-633f-4ee1-a7ce-ee7cf1f78284] Avinoam Singer PhD Candidate | Keating Lab Massachusetts Institute of Technology

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Joining models together in ChimeraX
by Christopher Camitta 10 Mar '22

10 Mar '22

Hi all, I am trying to join together two protein structures (in my case, one protein without the N-terminal domain combined with the NTD of a related protein). I came across a tutorial on how to do this in Chimera ( https://2019.igem.org/wiki/images/f/f3/T--UNSW_Australia--Daniel_Winter_Chi…), but from what I can tell ChimeraX's Build Structure tool doesn't have the options required to do this. Is there a way to join together two models in ChimeraX? Thanks, Chris

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ChimeraX
by Alejandro Amor 10 Mar '22

10 Mar '22

Hi there: I am trying to download ChimeraX for academic use and can't find a link to do it. Can you please provide some guidance? Thanks, Alex ______________________________ Alejandro Amor-Coarasa, PhD Assistant Professor of Nuclear Medicine in Radiology Director of the Radiochemistry Laboratory Albert Einstein College of Medicine 1300 Morris Park, 703-GB Bronx, NY 10461 Work: 718-430-3776 cell: 786-543-1534 e-mail: alejandro.amor(a)einsteinmed.org

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Analysis of the protein-ligand interactions using ViewDock
by Enrico Martinez 09 Mar '22

09 Mar '22

Dear ChimeraX users! I would like to use ChimeraX to calculate protein-ligand contacts established in docking calculations for the ensemble of the docking solutions (88 conformations of the ligand saved in multi-model format). Basically using the GUI of the UCSF Chimera previously I could do the following routine for the analysis of docking results: 1. Open the protein PDB 2. Use the Surface/Binding Analysis > ViewDock tool to open the docking poses 3. Using the Model Panel, select all docking poses 4. Use the Surface/Binding Analysis > FindHBond tool to locate all H-bonds. Make sure to check "Only find H-bonds with at least 1 end selected". You can check "write information to file" to save the H-bonds. May I adapt this protocol with the ChimeraX to perform such computing in batch (no-gui mode)? What should be the differences in the commands between Chimera and ChimeraX ( I've already seen that ViewDock is available in the ChimeraX as well...) Many thanks in advance! Cheers Enrico

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Unable to vary atomRadius by relative amounts
by Christopher Handelmann 04 Mar '22

04 Mar '22

Hi, I am trying to adjust the size of multiple individual residues in a molecule. I am attempting this with the "size [Target] atomRadius +[value]" command. When I run this, it doesn't perform a relative shift of each atom size in the residue but appears to set all atoms in the residue to an absolute size of the value. The documentation states that including the plus sign should make it a relative change. I am using ChimeraX 1.2.5. I appreciate your help figuring this out, Christopher Handelmann

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How to view consurf result in chimerax
by Shin, Yeonoh 03 Mar '22

03 Mar '22

Hello, I ran MSA in Consurf website, however I can not open the color-coded pdb result in Chimera or ChimeraX. When I click the link, attached error shows up. When I tried to open the link in chimeraX command line, another error shows up (attached). Could you tell me what I need to do to see the color-coded result in Chimera or X? Thank you. Yeonoh

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ChimeraX-users March 2022