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@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@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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/1bae62d955f4b9d6d05a31541af0372f11d365... . 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@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@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@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

---

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-- 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@takisbiotech.it

Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.takisbiotech.it&d=Dw...

D_.lgs. 196/03_

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