- ChimeraX-users - RBVI Mailing Lists

Surface dust command in the .cxc script
by 李泽 24 Feb '25

24 Feb '25

Hi all: I'm trying to use the .cxc script to run the software, I found that the "surface dust" command has never been executed in it. Have anyone met the same problem? Any suggestions. Thank you all. Best, Ze

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Freelance vs. Agency – Best Choice for Native App Developers Houston?
by hooria.khan＠algoace.com 23 Feb '25

23 Feb '25

I’m trying to decide whether I should hire a freelance developer or work with an agency for my native app development needs. Freelancers can be more affordable, but agencies offer structured project management. Are there any experienced <a href="https://algoace.com/houston-app-development/">Native App Developers Houston</a> who work independently and provide top-notch services? On the other hand, if you’ve worked with an agency, was the cost worth it? Any recommendations based on your experience?

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Update chain description from fasta file
by Paul Sauer 23 Feb '25

23 Feb '25

Hi, I really like the 'sequence update' feature that was introduced in Chimerax 1.9. I was wondering if it is possible to expand the capability of this command to update the sequence description/ sequence name from the header line of an opened alignment or fasta file and write it out with the cif file. It seems like currently the full sequence is updated from an associated fasta file but the sequence names are being ignored. Could the sequence name written into the ' entity.pdbx_description' column in the resulting cif file? Or maybe there is already an option that I missed? Also, as a secondary feature request, maybe the sequence update command could not only write the ' entity_poly.pabx_seq_one_letter_code_can' table but also use the available coordinates and residue names of the structure to write the '_entity_ poly.pdbx_seq,_one_letter_ code' table for each polymer that includes modified residues/ligands etc in parentheses in addition to the canonical one letter code where known. I could imagine that these capabilities would make depositing coordinates of macromolecular complexes with many chains to the PDB much easier and more interactive, so maybe this would be helpful for other people as well. Thank you to the Chimerax team & contributors for creating such a great program, Paul

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Dear ChimeraX users!
by amiraziznezhad＠gmail.com 23 Feb '25

23 Feb '25

Dear ChimeraX users! I am dealing with the analysis of protein-ligand interactions in a single PDB structure. I am looking for any tools implemented in Chimera-X, which could be used to analyse the interactions (besides the hbond and contact tools giving info in the log files msuic). I wonder to know which commands and corresponded ChimeraX tools could be used to produce the 2D contact diagrams shown on the Fig.4 as well as python graphs demonstrated on the Fig.5 in the Chimera-X article: https://www.myeasymusic.ir/ Many thanks in advance! Cheers Enrico

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RspProp
by Robert Stanley 23 Feb '25

23 Feb '25

Hello - I was wondering what I have to do to install the RspProp tool? It doesn't appear in my utilities menu or the structure analysis one. I have version 1.9 (2024-12-11). I very much appreciate this program and use it in my Biochem and Biophysical Chemistry courses to expose the students to it ASAP. Thanks, Bob Stanley Robert J. Stanley, Ph.D. Professor of Chemistry 1901 N. 13th St., 250B Beury Hall Temple University Philadelphia, PA 19122 (215) 204-2027 https://www.cst.temple.edu/~rstanley/

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Contribute to ChiemraX Recipe
by NG, Cheukhei Jackie [Student] 22 Feb '25

22 Feb '25

Dear ChimeraX Development Team, I am Jackie NG from a cryoEM group in the Hong Kong Polytechnic University interested in molecular visualization and analysis. I am writing to express my interest in contributing scripts to the ChimeraX library, specifically for inclusion in the ChimeraX Recipes. Sharing my scripts could benefit the community and enhance the utility of ChimeraX for various applications. The scripts are mainly quality-of-life improvements on copying selected parts of models, producing map-quality representations, organizing ligand chains, and many more. Please let me know if there is a process for submitting these scripts and any specific guidelines I should follow. I am eager to collaborate and contribute to the ongoing development of ChimeraX. Thank you for considering my contribution. I look forward to your response. Best regards, Jackie [https://www.polyu.edu.hk/emaildisclaimer/PolyU_Email_Signature-v2.jpg] Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.

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Aligning fasta sequence with the sequence of pdb model in chimeraX
by Rayees Mattoo 21 Feb '25

21 Feb '25

Hi, I was wondering if there is a way in chimeraX to align fasta sequence with sequence from the loaded pdb model. Just wanted to be sure that the residue numbering matches the original Uniprot sequence. Any other suggestions that can do the job quickly are welcome. Best, Rayees

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(no subject)
by FRANGIE Christian 21 Feb '25

21 Feb '25

Dear UCSF ChimeraX Support Team, My name is christian frangieh, I am currently using chimera x and i want to check the interacting residues that form the interface between 1 chain with 2 other different chains. for example my model has 3 chains (chain A,B,C) i want to have a list of the resideus of chain A and B that are interacting with chain C Can you please help me with this? Thank You

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save clipped volume
by Yanhe Zhao 20 Feb '25

20 Feb '25

Greeting there ChimeraX developer and community, I have "clip" used on my map and currently want to save the clipped one as a new mrc file, what is the best way to do this? I checked the "save Map" command and found the region option, but I don't think it is the right option if I have my clip plan tilt. Thanks a lot for any input. Thanks and cheers, Yanhe

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Help Needed with Building Capsid for ssRNA Homolog
by Bruno Hay Mele 20 Feb '25

20 Feb '25

Hi everyone, I am trying to build the capsid for a homolog of Chaetoceros socialis forma radians RNA virus 1 (PDB: 8b38). My approach was to work by homology, transferring the assembly/symmetry information from the PDB entry to my model, which I built by assembling homologs of the three subunits of 8b38. Unfortunately, this has not been as straightforward as I hoped. Ibm a complete newbie in this area, and my attempts to copy the relevant parts of the assembly information or use the ChimeraX bsymb tool have led nowhere. Could someone please point me to the right solution? Ibd really appreciate both: A practical solution: How to correctly transfer the symmetry information and generate the full capsid assembly in ChimeraX. Some references or explanations: Resources that explain why the solution works this way, so I can understand the underlying principles. Any help or pointers would be very much appreciated. Thank you very much for your time and assistance. Cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118

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ChimeraX Model Joining
by Nieder, Claire 20 Feb '25

20 Feb '25

Hey there, I am a grad student at UConn trying to covalently link two PDB models by inserting a GFP into the third intracellular loop of 5HT4. If you have any advice, I would really appreciate it. Thanks, Claire Nieder Kienzler Lab UConn Chemistry

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(no subject)
by FRANGIE Christian 20 Feb '25

20 Feb '25

Dear UCSF ChimeraX Support Team, My name is christian frangieh, I am currently using chimera x and i want to check the interacting residues that form the interface between 1 chain with 2 other different chains. for example my model has 3 chains (chain A,B,C) i want to have a list of the resideus of chain A and B that are interacting with chain C Can you please help me with this? Thank You christian

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Re: [Chimera-users] script for clashes
by Eric Pettersen 18 Feb '25

18 Feb '25

Hi Valerio, Well, one of the main motivations for using ChimeraX is that running commands actually return results instead of nothing. So the 'clashes' command returns a dictionary of the clashes, as described here: https://github.com/RBVI/ChimeraX/blob/1bae62d955f4b9d6d05a31541af0372f11d36… . Therefore you do not need all that extra code that Chimera needs to try to determine if there were any clashes. Instead it's just: clashes = run(session, "clashes") if clashes: # code for existing clashes else: # code for no clashes Now, reasonable structures should have at most a few clashes, and usually zero, not many thousands like your structures seem to have. I suggest opening one of the structures interactively in ChimeraX, run the "clashes" commands and look to see why there so many clashes. --Eric > On Feb 17, 2025, at 3:03 AM, chiarini(a)takisbiotech.it wrote: > > Dear Prof Pettersen, > > Thank you so much for your advice. So far I managed to operate in chimeraX and now I can see the outputs of my script. righ now I'm running the following: > > > # -*- coding: utf-8 -*- > > import os > from chimerax.core.commands import run > > # Funzione principale che accetta la sessione > def process_pdb_files(session): > # Specifica la cartella con i file PDB > folder_path = "C:/Users/utente/Desktop" # Modifica il percorso della cartella > > # Stringa da cercare nei file > search_string = "A3a" > > # Lista dei file PDB nella cartella > file_names = [fn for fn in os.listdir(folder_path) if fn.endswith(".pdb")] > > # Stampa dei file trovati nella cartella per debugging > print("File trovati nella cartella:", file_names) > > # Loop su ogni file che contiene 'search_string' nel nome > for pdb_file in file_names: > if search_string in pdb_file: > pdb_path = os.path.join(folder_path, pdb_file) > > # Apre il file PDB > print(f"Apertura del file {pdb_file}...") > run(session, f"open {pdb_path}") > > # Calcola i clash (comando corretto per ChimeraX) > run(session, "clashes") > > # Verifica se ci sono clash > clashes_found = False > for m in session.models: > if getattr(m, 'category', None) == "contacts": > clashes_found = len(m.pseudoBonds) > 0 > if clashes_found: > break > > # Se ci sono clash, elimina il file > if clashes_found: > os.remove(pdb_path) > print(f"Clash trovati, il file {pdb_file} è stato eliminato.") > else: > print(f"Nessun clash trovato per {pdb_file}.") > > # Chiude il modello dopo averlo processato > run(session, "close all") > > # Questa parte assicura che la funzione venga chiamata correttamente > def main(session): > process_pdb_files(session) > > # Quando esegui lo script in ChimeraX, la sessione viene passata automaticamente > main(session) > > AND I GOT THE FOLLOWING OUTPUT: > > runscript C:/Users/utente/Desktop/chimera_script2.pyFile trovati nella cartella: ['A3a_structure_1.pdb', 'A3a_structure_2.pdb', 'A3a_structure_3.pdb', 'A3a_structure_4.pdb', 'A3a_structure_5.pdb'] > Apertura del file A3a_structure_1.pdb... > open C:/Users/utente/Desktop\A3a_structure_1.pdb > Chain information for A3a_structure_1.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes84336 clashes > Nessun clash trovato per A3a_structure_1.pdb. > close allApertura del file A3a_structure_2.pdb... > open C:/Users/utente/Desktop\A3a_structure_2.pdb > Chain information for A3a_structure_2.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes655434 clashes > Nessun clash trovato per A3a_structure_2.pdb. > close allApertura del file A3a_structure_3.pdb... > open C:/Users/utente/Desktop\A3a_structure_3.pdb > Chain information for A3a_structure_3.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes626886 clashes > Nessun clash trovato per A3a_structure_3.pdb. > close allApertura del file A3a_structure_4.pdb... > open C:/Users/utente/Desktop\A3a_structure_4.pdb > Chain information for A3a_structure_4.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes482406 clashes > Nessun clash trovato per A3a_structure_4.pdb. > close allApertura del file A3a_structure_5.pdb... > open C:/Users/utente/Desktop\A3a_structure_5.pdb > Chain information for A3a_structure_5.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes315894 clashes > Nessun clash trovato per A3a_structure_5.pdb. > close all > > > WHAT ELUDES ME IS THAT FOR EACH STRUCTURE CHIMERA FINDS LOT OF CLASHES BUT THEN RETURNS THE STATMENT "NO CLASH FOUND FOR STRUCTURE X". Why is that? I know these structures have lots of overlapping atoms and it also seems that chimera counts the class "clashes". But maybe it also includes contacts? > I would like to count only steric clashes and atoms superposition which makes the structure impossible. > Thanks in advance for your help. > > Best regards, > > Valerio Chiarini > > Il 2025-02-12 21:06 Eric Pettersen via Chimera-users ha scritto: >> Hi Valerio, >> I should preface things by saying that this script would be >> considerably easier to write in ChimeraX, because in ChimeraX the >> "runCommand" equivalent actually returns results from the command >> instead of nothing. So in ChimeraX you can directly determine if the >> clash-finding command actually found any clashes. >> So clearly the body of your 'if' statement never executed since it >> includes illegal statements that would have produced errors if the >> body of the 'if' statement had been executed, whereas you got no >> output. So the first thing is put "print file_names" right after the >> line that sets files_names and see if any of the file names contain >> your search string ("xxx"). If none of them do, then you need to >> figure out why: is folder_path wrong?; is search_string wrong?; do the >> files not end in .pdb?; etc. >> In addition, I can see some problems even if the 'if' statement body >> had executed. You don't close the models at the end, so they will >> build up and "findclash" will find more and more clashes. Your actual >> findclash command needs to be "findclash #0 test self". There is no >> "chimera.clashClashList". Probably the simplest way to determine if >> clashes were found is checking if the clashes pseudobond group has any >> pseudobonds in it. You can do that with: >> for m in chimera.openModels.list(hidden=True): >> if getattr(m, 'category', None) == "contacts": >> clashes_found = len(m.pseudoBonds) > 0 >> break >> --Eric >> Eric Pettersen >> UCSF Computer Graphics Lab >>> On Feb 12, 2025, at 2:23 AM, valerio chiarini via Chimera-users >>> <chimera-users(a)cgl.ucsf.edu> wrote: >>> Dear Responsible, >>> I am working on a script that should iterate through several >>> structures, check the structures for clashes among all atoms, and >>> eliminate the pdb in any clashes are found. >>> Here is what I have worked out so far: >>> # -*- coding: utf-8 -*- >>> import os >>> from chimera import runCommand as rc >>> from chimera import replyobj >>> import chimera >>> # Specify folder >>> folder_path = "/gporq3/store_0/usr/chiarini/chroma/chroma/" >>> # String to be found >>> search_string = "xxx" >>> # List of files in the folder >>> file_names = [fn for fn in os.listdir(folder_path) if >>> fn.endswith(".pdb")] >>> print("File trovati nella cartella:" + str(file_names)) >>> # Loop on every file containing 'search_string' in the name >>> for pdb_file in file_names: >>> if search_string in pdb_file: >>> pdb_path = os.path.join(folder_path, pdb_file) >>> # Open the PDB >>> rc("open {}".format(pdb_path)) >>> # Calculates clashes >>> rc("findclash") >>> rc("wait") >>> # Verify if any clashes are found >>> clashes = chimera.clashClashList() >>> if clashes: >>> # If clashes are found eliminates the file >>> os.remove(pdb_path) >>> print("Clash trovati, il file {} è stato >>> eliminato.".format(pdb_file)) >>> else: >>> # If no clash, exit normally >>> print("Nessun clash trovato per {}.".format(pdb_file)) >>> But no analisys is done at all. I have been searching through the >>> script page (https://www.rbvi.ucsf.edu/trac/chimera/wiki/Scripts) in >>> order to found some clue on this function but so far I have found >>> none. >>> Could you help me on this issue? >>> Thank you in advance >>> Valerio Chiarini _______________________________________________ >>> 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/ > > -- > Dr. Valerio Chiarini > > _Senior Scientist_ > > Proteins & Monoclona Antibodies Department – Takis Biotech > > c/o Tecnopolo > > Via di Castel Romano, 100 > > 00128 Rome, Italy > > Tel.: +39 06-50576077 > > Fax: +39 06-50576710 > > Email: chiarini(a)takisbiotech.it > > Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.takisbiotech.it&d=D… > > D_.lgs. 196/03_ > > _Le informazioni contenute in questa comunicazione e gli eventuali > documenti allegati hanno carattere confidenziale, sono tutelate dal segreto > professionale e sono ad uso esclusivo del destinatario. Nel caso questa > comunicazione Vi sia pervenuta per errore, Vi informiamo che la sua > diffusione e riproduzione è contraria alla legge e preghiamo di darci > prontamente avviso e di cancellare quanto ricevuto. __Grazie._ > > _This e-mail message and any files transmitted with it are subject to > attorney-client privilege and contain confidential information intended > only for the person(s) to whom it is addressed. If you are not the intended > recipient, you are hereby notified that any use or distribution of this > e-mail is strictly prohibited: please notify the sender and delete the > original message. __Thank you._ >

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Bundle development for chimeraX - svg onClick event to run command from QWebEngineView
by Lou Holland 18 Feb '25

18 Feb '25

Hello, Apologies if this is the wrong email address to contact about this. I am currently working on a privateer bundle for carbohydrate validation in chimeraX. At present, I have it so that the privateer tool will display SNFGs of glycans present in the structure using svgs displayed in a QWebEngineView(). I would like, if possible, on clicking elements of the svg to run a chimeraX command (view /chainID:resID) to centre the view window on the residue in question. At present, I can implement an onClick event to display the command that should be run, but haven't managed to figure out how to just run the command from within that QWebEngineView. Is there a mechanism already in place for doing something like this that I could take advantage of? I'd considered using the "log html" to display the svgs in the log instead of the WebEngineView() so that I could take advantage of the href="cxcmd" functionality, but the svgs are long, with semicolons and new-line characters which interfere with this. Best wishes, Lou Holland (Pronouns: they/them) Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK

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Assistance with ChimeraX Syntax for SPRITE Hands-On Module
by Zeenat Bashir 18 Feb '25

18 Feb '25

Dear ChimeraX Developers, I hope this email finds you well! I am currently developing a hands-on module for my students on visualizing SPRITE results using ChimeraX. However, I am facing an issue with the syntax for aligning the residues of *2HNT* with *1A0J*. The module I am using, which was provided by Basil (attached with this email), includes syntax for Chimera (refer to Figures 10 and 11 in the attached document). I have tried adapting the syntax for ChimeraX but have not been successful. I would really appreciate your guidance on this matter or if you could direct me to someone who might be able to assist in generating the correct command line syntax. Thank you so much for your time and help! Zeenat -- *Dr. Zeenat Bashir* *Senior Lecturer* *Biotechnology Lab Coordinator* *Department of Chemical and Biomolecular Engineering* *University of Pennsylvania* *310 Towne Building* *220 S. 33rd Street* *Philadelphia, 19104 -6393* bashirz(a)seas.upenn.edu

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Roll command for multi objects in grid
by Enrico Martinez 18 Feb '25

18 Feb '25

Dear ChimeraX users! Using til command I split six superimposed structures, displaying them as the 2x3 table and then rotate each object along its axis within each grid using "roll" in the following way: # for 6 different object roll models #1 center #1 & protein roll models #2 center #2 & protein roll models #3 center #3 & protein roll models #4 center #4 & protein roll models #5 center #5 & protein roll models #6 center #6 & protein Would it be possible to simplify this to one "roll" command that will automatically rotate all displayed objects in the separate grids along its axis ? Many thanks in advance Enrico

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Questions about match and view commands
by Enrico Martinez 16 Feb '25

16 Feb '25

Dear ChimeraX users! I am performing a visualization of the ensemble of conformers for the same protein defined in the chimerax as models #1 to #6. Here are some of my questions: 1 - I try to superimpose all structures to the first model using match #2-5 to #1 is it possible to use some regular expression instead of #2-5 to select all models from the second to the last e.g. to superimpose all structures to the first one in the script. 2 - I try to automatically orient the superimposed models along its principal axe in one command e.g. using view orient but it does not produce a proper orientation. What kind of trick could work for a nanobody object to orient it automatically e,g, along Z ? Many thanks in advance Enrico

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assistance on bundle writting
by Nguyen, Catherine 14 Feb '25

14 Feb '25

Hello, I was hoping to get your help. I am trying to write a bundle and I am struggling to figure out how I can add psuedo-bonds using python as I want to connect two amino acids by the CA. Would you be able to help me find a way to do this? I hope to hear from you soon, Best wishes, Catherine

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MUNKI Managed Software Download URL
by Antony Nelson 14 Feb '25

14 Feb '25

Hi, I appreciate this might seem an odd request, but do you have a public download location for ChimeraX software? There exists a widely used system by which administrators of Apple computers distribute software to their users by means of applications known as Munki and Autopkgr. Software which can be downloaded from public websites can be managed in such a way that new releases and updates are automatically added to the software repository Apple administrators curate for their users. Without making this publicly available, admins will only update your software when users request the admins to do so. Looking back on the Loupe Browser instances that have been made available to my users, they have only had access to versions: 0.8.0 0.9.0 0.9.1 0.93.0 1.1.1 1.7.1 and today they will have 1.9.0 If your software was made available via public download by a predictable URL, then they would have had access to every version released on the day it was added to your website since it was first requested by users. If you are concerned about the acceptance of terms of conditions then perhaps this could be incorporated into the URL string. Regards

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How to get different silhouette widths for 2 maps
by Hong ZHAN 13 Feb '25

13 Feb '25

Hi there, I am trying to create a video with two maps overlay with different silhouette widths. It is easy to do with 2 images, but how I can do it in a video setting? If I change the width to 6, all maps changes the width to 6. Thanks! -Hong

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Unable to load scripts at startup
by Pranav Shah 13 Feb '25

13 Feb '25

Hi Team, (I accidentally sent this to ChimeraX-bugs, copying it again here) I am trying to load some scripts at startup via the chimerax_custom_functions.cxc command file - open /Users/ps/.chimerax/chimerax_commands/chimerax_custom_functions.cxc in the log file I see the following message: still retrieving bundle list from toolshed open /Users/ps/.chimerax/chimerax_commands/chimerax_molmap_cube.py Error running startup command 'open /Users/ps/.chimerax/chimerax_commands/chimerax_custom_functions.cxc': Unknown command: open /Users/ps/.chimerax/chimerax_commands/chimerax_molmap_cube.py This is strange as simply running "open /Users/ps/.chimerax/chimerax_commands/chimerax_molmap_cube.py" in the ChimeraX command panel runs perfectly fine! the error occurs only when I try to run that line through the .cxc file. Am I missing something? or could this be a bug? I am on the stable release of ChimeraX (version 1.9). Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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PAEcontacts colorkey
by ccinsua＠gmail.com 13 Feb '25

13 Feb '25

Hi all, Thank you very much for your work with chimerax. I've been using it to study alphafold complex prediction, and I find the command alphafold contacts very useful. The default color key (guess it is paecontacts, according to documentation) ranges are blue (low PAE) - green (medium PAE) - yellow (high PAE). However, I am unable to add a color key using "key paecontacts". Somehow I have to define it myself. Is there anything I am missing? I would like to stick to the blue-green-yellow scheme. Thanks a lot in advance Carlos

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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]

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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

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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.

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