- ChimeraX-users - RBVI Mailing Lists

NASA - Country of Origin Statement and 508 Conformance Request: UCSF ChimeraX
by Price, Dru C. (LARC-B730)[eMITS] 12 Feb '25

12 Feb '25

Hello, my name is Dru and I work for the NASA Commercial IT Acquisition Team. As such, I ensure that all NASA acquisitions of Covered Articles comply with Title II; General Provision Section 208 and Title V; General Provisions Section 514 of the Consolidated Appropriations Act, 2021, Public Law 116-260<https://www.congress.gov/bill/116th-congress/house-bill/133/text>, enacted December 27, 2020. To do so, the Country of Origin (CoO) information must be obtained from the company that develops, produces, manufactures, or assembles the product(s). Please specifically identify the country, or countries, in which each of the following software products is developed and maintained: * UCSF ChimeraX Additionally, if available, please identify all authorized resellers of the product(s) in question. Finally, I am requesting an Accessibility Conformance Report (starting from Page 10 of the attached VPAT) be completed and returned so that NASA can assess the product's level of 508 Conformance. More information regarding Section 508 of the Rehabilitation Act of 1973 and what it means to manufacturers/developers can be found at https://www.section508.gov/sell/vpat. I have attached a blank copy of the latest revision of the VPAT standard if you do not already have a completed VPAT available for this product. Please complete this document to the best of your abilities, if one is not already available. Product / Service Description Model Number Country of Origin Is final testing performed in the United States? Please let me know if you have any questions. Thank you, Dru C. Price Procurement Analyst eMITS | [ROTHE ARES JV] Commercial IT Management Support Croscutting Agency Service (CAS) Branch Enterprise Business Management Office (EBMO) NASA - Office of the Chief Information Office (OCIO) [cid:image001.png@01DB7D5D.40BD4D20]<https://teams.microsoft.com/l/chat/0/0?users=dru.c.price@nasa.gov> [cid:image002.png@01DB7D5D.40BD4D20]

3 3

ChimeraX fetch by PubChem CID
by Elaine Meng 12 Feb '25

12 Feb '25

> On Feb 12, 2025, at 11:41 AM, Alexander Mansueto <alexander.j.mansueto(a)vanderbilt.edu> wrote: > > Can we import pubchem CID molecules to model proteins with lipids? Would be very cool. Hi Alexander, The recommended address for asking ChimeraX questions is the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> mailing list CC'd here, see "contact us" on our website or in the ChimeraX menu: <https://rbvi.ucsf.edu/chimerax/docs/contact.html> If PubChem Compound has the coordinates, you can open them in ChimeraX by CID, e.g. command open pubchem:12123 - OR - open 12123 from pubchem ... as explained here <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> ...or with menu: File... Fetch by ID, choosing the Pubchem option and specifying the CID in the dialog: <https://rbvi.ucsf.edu/chimerax/docs/user/fetch.html> However, not every entry in PubChem Compound has coordinates available, so I don't know if it will work for your specific molecules of interest. 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

1 0

Get color code of a custom color
by Ahmad Khalifa 11 Feb '25

11 Feb '25

I created a custom color that I want to use in a different session. is there a way to do that besides trying to match colors by eye? Regards.

5 4

steam VR running but still get an error with Vr on command.
by Krishnan Raman 10 Feb '25

10 Feb '25

[cid:5bbc0381-58d6-4058-bc7c-183bcd144645] Steam VR is running and still i get this error. Am i overlooking something? thanks Krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 1

there is no amination？？？
by 刘涛 07 Feb '25

07 Feb '25

2 2

Recording MD Trajectory Movie in ChimeraX
by Gourav Das 07 Feb '25

07 Feb '25

Dear ChimeraX users, I have performed MD simulation of a system using AMBER20. The topology and trajectory files are in .parm7 and .nc formats, respectively. I would appreciate your guidance on visualizing and recording the trajectory as a movie in ChimeraX. Thank you for your support. With regards, Gourav Das Research Scholar Department of Chemistry Indian Institute of Technology Kharagpur West Bengal, India-721302 Mob: +91-6295251060 --

2 5

Double and Triple Bond Stick Style
by Smith, Chase 05 Feb '25

05 Feb '25

Dear ChimeraX, I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms. Thank you, Chase Smith ... ChaseSmith, PhD Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry School of Pharmacy MCPHS University 19 Foster Street | WorcesterMA01608 T 508.373.5717F 508.890.5618C 978.855.7203 chase.smith(a)mcphs.edu www.mcphs.edu MCPHS University Confidentiality Note: This e-mail, and any attachment to it, is intended to be confidential and might be legally privileged. It is intended solely for the use of the addressee. If you are not the intended recipient, you are hereby notified that reading, copying, disseminating or distributing this email is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.

5 5

Re: Introduction of a proteolytic cleavage in ChimeraX
by Elaine Meng 04 Feb '25

04 Feb '25

> On Feb 4, 2025, at 3:30 AM, Mark Hilge <markhilge(a)icloud.com> wrote: > > Dear Dr. Meng, > [... details removed ...] > Question: In ChimeraX, is there a possibility to introduce a proteolytic cleavage between say Leu112 and R113? This should result in Leu112 with a carboxylate group followed by a TER keyword. > > Many thanks in advance! > Kind regards, > Mark Dear Mark, It depends what you want to use this for. If it's just for a figure, that is totally different than if you were going to do some extensive workflow afterwards. If you have an input PDB file, one "dumb" way is to text-edit it to put the TER card in before opening in ChimeraX. However, that will not add a carboxylate oxygen, there would just be a dangling C=O. If you wanted an OXT you would have to add it "manually," e.g. in the Build Structure tool. However, that will be problematic because it won't want to add the OXT right on top of the N, which is where it would want to go. You'd also have to change the conformation of the chain, e.g. rotate a bond with the mouse mode or the "torsion" command. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html> Within ChimeraX, you could use command ~bond to remove bonds. However, if you do this within a chain defined in the input (e.g. PDB SEQRES lines or mmCIF file equivalent), it will then draw a dashed line because it still "knows" they are supposed to be connected within the chain because of the SEQRES records in the PDB file. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> So it's all more complicated than you might think, especially if you wanted everything to be correct for some subsequent modeling workflow. You might instead give the two parts two different chain IDs. One way is to text-edit the PDB file. Another is to open the thing twice, delete the first part of the chain in one copy, delete the other part of the chain in the other copy, and then use "combine" to create a new model that has both parts but with different chain IDs, and then use "save" to save a PDB file of that combined model. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> However, you would still need to text-edit the PDB file manually so that there are SEQRES records for the two different chains (the two parts of the original single chain) that each contain only the residues for the corresponding part. These are different than the ATOM records that have the coordinates. And I can't even begin to explain how you might do it in mmCIF, all of this is in PDB format only. So if you bothered to do all that, then if you use "addh" it will automatically add the "OXT" because it will finally recognize the new cleaved C-terminus as a real C-terminus. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/addh.html> For future reference: please use chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here to ask questions about ChimeraX, omitting any information that needs to remain private. If you send email to me only, it may not get answered. Thanks, 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

2 1

Suppress errors when using runscript?
by Vorländer,Matthias Kopano 03 Feb '25

03 Feb '25

Hi, I wondered if it is possible to suppress/ignore an error message when executing scripts with runscript. Specifically, I have a script to analyze alphafold (3) predictions and select residue interfaces residues using the interface select command. The selection for each of the five model is then saved in a named selection: # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection for the interface residues. name frozen interface_residues$2_model_4 sel This works fine when all models show contacts , however, if one of the models/predictions does not have any residues involved in an interface, the script stops with the error “Nothing is selected by the specifier”. It would be great if the script does not pause at this message. Below the full .cxc script I am using: Best, Matthias # Generate AF contacts for all predictions of an AF3 run # # Usage: # runscript analyse_af3_prediction.cxc <AF_screen_directory> <custom_prediction_name> # The script assumes that five models were generated by AF. It expects the CIF files to be in a sub‐directory # matching the pattern "*model_X*.cif" and the corresponding JSON files in a sub‐directory matching "*data_X*.json" # for each model number X (4, 3, 2, 1, 0). # For the alignment and mseries slider command to work properly, the script assumes no other models are open. echo "Usage: runscript analyse_af3_prediction.cxc <AF_screen_directory> <custom_prediction_name>" ##### Model 4 ##### # Open the structure and its JSON scores for model 4. open $1/*model_4*.cif open $1/*data_4*.json structure last-opened hide show c # Generate AF contacts (using JSON scores) for chain A (or the first chain) alphafold contacts last-opened &/A name model_4_af_contacts_$2 # Create pseudobonds for the contacts and label them with residue names and numbers. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation to a file. save $1/af_contacts_model_4_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_4_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection for the interface residues. name frozen interface_residues$2_model_4 sel show interface_residues$2_model_4 style interface_residues$2_model_4 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_4 saveFile $1/interface_residues$2_model_4_buriedArea_300.txt # Color the model for clarity. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_4 and info saved to $1/interface_residues$2_model_4_buriedArea_300.txt" ##### Model 3 ##### # Open the structure and its JSON scores for model 3. open $1/*model_3*.cif open $1/*data_3*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation. save $1/af_contacts_model_3_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_3_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_3 sel show interface_residues$2_model_3 style interface_residues$2_model_3 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_3 saveFile $1/interface_residues$2_model_3_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_3 and info saved to $1/interface_residues$2_model_3_buriedArea_300.txt" ##### Model 2 ##### # Open the structure and its JSON scores for model 2. open $1/*model_2*.cif open $1/*data_2*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation. save $1/af_contacts_model_2_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_2_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_2 sel show interface_residues$2_model_2 style interface_residues$2_model_2 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_2 saveFile $1/interface_residues$2_model_2_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_2 and info saved to $1/interface_residues$2_model_2_buriedArea_300.txt" ##### Model 1 ##### # Open the structure and its JSON scores for model 1. open $1/*model_1*.cif open $1/*data_1*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_1 sel show interface_residues$2_model_1 style interface_residues$2_model_1 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_1 saveFile $1/interface_residues$2_model_1_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_1 and info saved to $1/interface_residues$2_model_1_buriedArea_300.txt" ##### Model 0 ##### # Open the structure and its JSON scores for model 0. open $1/*model_0*.cif open $1/*data_0*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation. save $1/af_contacts_model_0_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_0_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_0 sel show interface_residues$2_model_0 style interface_residues$2_model_0 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_0 saveFile $1/interface_residues$2_model_0_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_0 and info saved to $1/interface_residues$2_model_0_buriedArea_300.txt" ##### Final Steps ##### # Move all models (except the last-opened) to a common group (optional) mm #*&~last-opened&/A to last-opened&/A # Create an mseries slider for the five models. mseries slider #1-5 title $2 name $2_slider mseries #1-5 echo "Use the slider to go through the models!" echo "Pairwise contacts (based on the JSON fle) and all residues involved in an interface (based on a buried surface are of 300 Angstrom or more) have been saved in the input folder for each prediction" echo "You might want to increase stringency by calcualting the overlap between all predictions"

2 1

Getting two color keys in the same ChimeraX session
by Elaine Meng 03 Feb '25

03 Feb '25

> Begin forwarded message: > > From: Eric Pettersen via Chimera-users <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] Re: key command > Date: February 3, 2025 at 11:52:12 AM PST > To: Fabian Glaser <fglaser(a)technion.ac.il> > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Reply-To: chimera-users(a)cgl.ucsf.edu, Eric Pettersen <pett(a)cgl.ucsf.edu> > > Hi Fabian, > There is no direct support for multiple keys, but it is pretty easy to “trick” ChimeraX into showing multiple keys. You would create your first key normally, getting it exactly the way you want it to look before creating the next key. You create the next key with the following Python code: > > from chimerax.color_key.model import ColorKeyModel > m = ColorKeyModel(session) > > If the above was in a file ending in ‘.py’, you could just use the ‘open’ command to run it and create the key. I’ve attached a file with that code in it for convenience. Once you have created the key, then all operations that affects keys (like the ‘key’ command) will affect the new key and leave the original key as is. If you had the Color Key tool up, it will continue to show the old values. Just close it and re-open it to show the new values. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >> On Feb 3, 2025, at 6:31 AM, Fabian Glaser via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >> >> Hi, >> >> We would be interested to add more than one key color bar in the same chimerax session. But we noticed the key command allows only one color key can be present at a time. >> >> Is there a way to add more than one color key in the same session? >> >> Thanks a lot, >> >> Fabian >> >> >> Fabian Glaser, PhD >> >> Technion Centre for Structural Biology (TCSB), Computational Section, Head >> Technion Human Health Initiative (THHI) >> Technion - Israel Institute of Technology, Haifa, Israel >> fglaser(a)technion.ac.il >> +972 (0)48293701 >> >> >> >> _______________________________________________ >> Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu >> To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/ > > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

1 0