Hey Dimitry,
The "quiet" option (if present) is set to zero by default for parsed
PyMOL commands, but is not set for Python API calls.
align
is nearly equal to
cmd.align(quiet=0)
Thus, if you want to get rmsd output, include quiet=0 and run your
script with output redirection.
The last line of your script should read
cmd.align(pdb.group(1) , '1gk9', quiet=0)
and the script should be called like this:
pymol -qa script > output
That's at least how it used to work.
Andreas
DimitryASuplatov wrote:
Hello,
with your help I was able to write the following script to automatically
load 21 structure and align 20 of them to the remaining one.
*************************************************
import os
import re
from os.path import join, getsize
cmd.delete(all)
p = re.compile('[A-Za-z\.]*pdb')
w = re.compile('nowater')
for root, dirs, files in os.walk('./'):
for file in files:
<------>if p.search(file) and w.search(file):
<------> cmd.load(file)
cmd.delete('1gk9*')
cmd.fetch('1gk9')
for file1 in files:
<------>if p.search(file1) and w.search(file1):
<------> if re.search('1gk9', file1):
<------><------>continue
<------> pdb = re.search('(.+)\.pdb', file1)
<------> print pdb.group(1), ' and 1gk9'
<------> cmd.align(pdb.group(1) , '1gk9')
*************************************************
The problem is that I see only the result - aligned structures. But I
want to see the RMSD values and apply them to scrip variables. Is that
possible?
Thank you.
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Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
