Thank so much Jared!
So here is modified script:
#!/bin/bash
pdb="./NpXynWT_apo_340K_MD_multi_0434.pdb"
LENGTH="$(pymol -cQ -d "
from pymol import cmd
load ${pdb}, tmp
sel = 'tmp and polymer'
print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom])))
")"
echo $LENGTH
I guess it's a problem with the -cQ flag because without it your
script gives me the full output, while I echoes the variable:
PyMOL(TM) Molecular Graphics System, Version 1.7.2.1. Copyright (c)
Schrodinger, LLC. All Rights Reserved. Created by Warren L. DeLano,
Ph.D. PyMOL is user-supported open-source software. Although some
versions are freely available, PyMOL is not in the public domain. If
PyMOL is helpful in your work or study, then please volunteer support
for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support
subscription. More information can be found at "http://www.pymol.org";.
Enter "help" for a list of commands. Enter "help <command-name>" for
information on a specific command. Hit ESC anytime to toggle between
text and graphics. Command mode. No graphics front end. Detected 20
CPU cores. Enabled multithreaded rendering. PyMOL> PyMOL>from pymol
import cmd PyMOL>load ./NpXynWT_apo_340K_MD_multi_0434.pdb, tmp
CmdLoad: "./NpXynWT_apo_340K_MD_multi_0434.pdb" loaded as "tmp".
PyMOL>sel = 'tmp and polymer' PyMOL>print(len(set([(i.chain, i.resi,
i.resn) for i in cmd.get_model(sel).atom]))) 219 PyMOL: normal program
termination.
however with -cQ it gives me nothing :-)
Hey Blaine,
your script is very usefull but it does not work in my case.
1) fetch command gives me an error (which is not the case of "load"
probably because I have outdated pymol).
2) I need to load pdbs inside of my shell script, meaning that I am
looping a folder by bash routine and use it then with pymol to measure
the length of PDB and save it as the variable (in bash!!), which is
expected to be used on the next step...
james
пн, 24 июн. 2019 г. в 18:53, Jared Sampson <jared.samp...@columbia.edu>:
>
> Hi James -
>
> Try this, assigning to new variable LENGTH by using -Q flag to suppress other
> output, and running in a subshell (untested, and assuming Bash):
>
> ```
> pdb="./NpXynWT_apo_340K_MD_multi_0434.pdb"
> LENGTH=$(pymol -cQ -d "
> from pymol import cmd
> load ${pdb}, tmp
> sel = 'tmp and polymer'
> print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom])))
> ")
> ```
>
> Hopefully that works, or at least gives you an idea of how it might be done.
>
> Best,
> Jared
>
>
> On June 24, 2019 at 12:08:07 PM, James Starlight (jmsstarli...@gmail.com)
> wrote:
>
> pdb="./NpXynWT_apo_340K_MD_multi_0434.pdb"
> pymol -c -d "
> from pymol import cmd
> load ${pdb}, tmp
> sel = 'tmp and polymer'
> print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom])))
> "
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