Hello all,
I want to calculate RMSD for my docking protein models. So I have one target
model and one docked model. Each model has a larger chain called receptor,
and a smaller chain called ligand. The chains in docked model is highly
sequentially similar to the corresponding chains in the target
Dear PyMOL Users,
Please join me in congratulating Michael Lerner, PhD, for being
awarded the Warren L. DeLano Memorial PyMOL Open-Source Fellowship for
2010--2011. As many of you are undoubtedly aware, Michael developed
the APBS plugin for PyMOL. Out of the nearly 11,000 APBS users
world-wide, mo
Hi all,
I am using pymol to monitor the structure evolution of one protein which could
be bound to some fixed points on a spherical surface. However, I have no idea
about how to incorporate these active points in pymol. Any suggestion is
welcome. Thanks in advance.
Cheers,
Jay
I use these commands:
cmd.reset()
cmd.origin(position=[0,0,0])
cmd.center("origin")
cmd.move('z',-cmd.get_view()[11])
Raluca
On Thu, 09 Sep 2010 12:11:52 -0400
Philip Bransford wrote:
> I am using PyMOL to generate a mesh of a protein. My
>commands look like
> this:
>
> load prot.pdb
> sh
I am using PyMOL to generate a mesh of a protein. My commands look like
this:
load prot.pdb
show surface
save surf.obj
The mesh surf.obj (or surf.wrl) is rotated and translated relative to
the atomic coordinates in prot.pdb. Is there some way to prevent this
from happening? For my application
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Jason,
It was 0.99. I have re-checked using 1.2 and everything is displayed correctly.
Sorry about that.
Vitaly
- Original Message -
From: Jason Vertrees
Date: Thursday, September 9, 2010 8:57 am
Subject: Re: [PyMOL] CA trace
Cc: pymol-users@lists.sourceforge.net
> Vitaly,
>
> I just
Vitaly,
I just ran your example and I get two separate chains. What version
of PyMOL are you using?
Cheers,
-- Jason
On Thu, Sep 9, 2010 at 12:16 AM, Vitaly Vostrikov wrote:
> Hello,
>
> I would like to show a CA trace for each of the chains in a dimer. The
> "cartoon_trace" option works fin
