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/1bae62d955f4b9d6d05a31541af0372f11d36536/src/bundles/clashes/src/clashes.py#L76 .  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 _______________________________________________
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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=DwIDaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=AnLbjfzj4A4gVWflERdQcNZUEpTJryfgdkg4779VL5A&m=WctdkVI3bU6ZB5AYRFX4pbJDI1WGXn1cYThIb5wbBX6IOMa74PN_emRBlFkbG2xv&s=ntuB_R3Y28Ozj_g3c42dM-o31hWODDm2cffJPyeyfbE&e=

D_.lgs. 196/03_

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