Hi Shubham,
It seems like a deficiency of the 'info' command that it can't put the information directly into a file.  We will look into rectifying that -- and yes, the problem is that the Log does not exist in nogui mode.  However, since you are using a Python script for this (rather than a Chimera command script), you can save the information directly to a file yourself.
Replace:

run(session, "info residue sel")
run(session, "log save aromatic_list.html")

with:

from chimerax.atomic import selected_residues
with open("where-I-want-to-save.txt", "w") as f:
for r in selected_residues(session):
print(r, file=f)

You can do similar things with distances and angles because the commands return the distance/angle values, e.g.:

d = run(session, "distance atom1 atom2")
write/append d to a file

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On May 10, 2022, at 3:29 AM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,
I hope you are doing well.
I have a python script (myscript.py) as follows:
 
from chimerax.core.commands import run
import os
os.chdir("C:\\Users\\Shubham\\Desktop")
run(session, "open C:\\Users\\Shubham\\Desktop\\PDB_Script\\1ebt.pdb")   # location of my pdb file
run(session, "sel aromatic & protein")    
run(session, "log clear")
run (session, "info residue sel")
run(session, "log save aromatic_list.html")
 
I am using the following prompt for calling chimerax from command prompt:
Gui enabled:   chimerax --script C:\\Users\\Shubham\\Desktop\\myscript.py
Gui disabled:   chimerax --nogui --script C:\\Users\\Shubham\\Desktop\\myscript.py
 
With gui mode enabled, the html file, aromatic_list.html, is created.
However, when disabling gui, nothing is created. 
 
I suspect this is because I am relying on the log which may not be functional when gui is disabled?
Is there a way of redirecting the output of certain commands (e.g info, distance, angle) to a desired text file when disabling gui?
I tried with sys.stdout but it did not work (empty text files were created.).
 
Regards,
Shubham
 
Sent from Mail for Windows
 
_______________________________________________
ChimeraX-users mailing list
ChimeraX-users@cgl.ucsf.edu
Manage subscription:
https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users