February 2025 - ChimeraX-users - RBVI Mailing Lists

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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