I'll second that.
While applying PyMOL to generate millions of molecular renderings in an
automated fashion may be a cool demonstration of open-source databases &
technology, using 2D molecules as inputs kind of misses the point:
PyMOL is a 3D viewer, optimized for depicting 3D representatio
Hi there,
The gallery is currently in 2D format. Any plans to generate 3D galleries?
J
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand
Pukeka Matua
Te Kura Taiwhanga
I have automated the process to make molecule galleries, which I am
finding very useful to my research, so I thought that I would share the
opportunity and take requests. It is quick and easy. I did a bisphenol
search today, and as I expected, the search turned up a few stilbenes,
which is the s
Hello,
I have found a pymol wiki article about CEalign
(http://www.pymolwiki.org/index.php/Cealign) - structure alignment
procedure that is claimed to be better than align and super since it
primarily aligns structures, not sequences.
I did not find any API for CEalign. Does anybody now how could I
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 lin
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
