[chimerax-users] no gui mode and redirecting output of some commands

[Eric Pettersen]

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 at 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 <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows
>  
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