Hi James,
Just a follow up, I would still recommend you use the script in a file to do
this as it is less messy but it can be done:
pymol -c -d '
from pymol import cmd
cmd.load("A.pdb")
cmd.load("B.pdb")
cmd.load("C.pdb")
cmd.super("C*","A*")
cmd.super("B*","A*")
cmd.bg_color("white")
cmd.save("output.pse")
'
If you paste the above as is in shell It should work provided you are the
directory containing the 3 pdb files
Executing pymol with -d flag in shell means you can input pymol commands, to
get around indentation you can run leave an ' apostrophe at the end to paste
the scripts in and execute all as a string without needing to save as a file
Just for reference, the -c flag is "batch processing (no GUI)" and the commands
above can be saved into a python file and ran using:
pymol -c -r "path_to_script"
Hope this helps.
Cheers,
Ali
________________________________________________________________
Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
Email: [email protected]
On 23/6/19, 7:00 pm, "James Starlight" <[email protected]> wrote:
hello there,
As a part of my scripting routine, I would like to use pymol in no-gui
mode (directly in the linux shell) to do the following things:
1) load in pymol 3 conformations of the same protein, which are
defined as A.pdb B.pdb C.pdb
2) superimpose C to A using "super" or alternatively (which is better)
"alignall" to A
3) change background of the session to white :-)
4) save the pymol session for the superimposed A B and C as the *.pse
output file
could you suggest me 1 string command for pymol, which I can directly
use in shell terminal to do the mentioned routines in no-gui mode?
thanks you!!
James
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