Hi Thomas,
I assume components.cif is the same file that I've just downloaded for
LigPlot+. Would it be possible that PyMOL automatically finds this
file, say by reading $compcif or some such variable?
Thanks.
Andreas
On 16/10/2014 10:08, Thomas Holder wrote:
> Dear all,
>
> this is for t
Hi Jared,
Thanks for your help. I have two issues with this script:
1. It only works once after I've started pymol; the second time, python.exe
crashes.
2. It does create an object with *distances*, not the actual residues.
Your other solution with the single word selectors should work but
Dear all,
this is for those who like to use the latest Open-Source PyMOL code from SVN.
We replaced the slow python mmCIF reader with a very fast and efficient C++
implementation. Other than being much faster, this implementation provides:
- new connect_mode=4 does bonding with components.cif d
sure, you are welcome to update the PyMOLWiki page.
Cheers,
Thomas
On 16 Oct 2014, at 15:57, Markus Heller wrote:
> Aha, that makes sense now.
>
> Would it be worth to clarify this in the pymolwiki
> (http://www.pymolwiki.org/index.php/Show)? That's where I got my version
> from ...
>
>
Aha, that makes sense now.
Would it be worth to clarify this in the pymolwiki
(http://www.pymolwiki.org/index.php/Show)? That's where I got my version from
...
Cheers
Markus
-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com]
Sent: Thursday, October 16, 2014
Hi Markus,
> # hide non-polar hydrogens
> hide (h. and (e. c extend 1))
This will hide all representations -- including surface -- for non-polar
hydrogens. I guess what you rather want is to remove those non-polar hydrogens,
so that they will not be included in the surface calculation.
# remo
Thomas,
If you comment out the h_add line in the pml script below, the surface looks
good. If it's in there, it's broken for me.
Cheers
Markus
# load the PDB file
fetch 3CIY, async = 0
# add hydrogens
h_add
# hide everything but show cartoon
hide lines
#as cartoon
# show protein surface
Hi Markus -
First, you need to run the python script from the wiki page (save it as, e.g.
polarpairs.py). Then, to run pure Python code within a pml file, you’ll need
to enclose those lines in a python block
(http://www.pymolwiki.org/index.php/Python) using ‘python’ and ‘python end’.
For exa
