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
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