Just to quickly add... probably the easiest way to run CE at the present
might be through the new protein comparison tool at RCSB-PDB web site:
http://www.rcsb.org/pdb/workbench/workbench.do
Andreas
On Tue, Dec 8, 2009 at 8:12 AM, Michael Zimmermann wrote:
> Dr. Vertrees, thank you for the th
Michael,
You are correct. Users can just download the CE program and use that. The
CEAlign that I was talking about is a C++ extension that I wrote just for
PyMOL. It plugs directly into the PyMOL system so you can just type:
cealign protA, protB
and the proteins are aligned and the results a
Hi,
I posted an answer on the blog, but I'll copy it here. Someone can correct
me if I'm wrong!
On Tue, 08 Dec 2009 10:02:59 -0600 Michael Zimmermann
wrote:
> I have no experience with fuse, but my guess would be Mariana might
> want to just use 'bond' and translate one termini as needed. If
Dr. Vertrees, thank you for the thorough reply to Saeid's question. I just
wanted to note that you don't have to install all of PyMol from source to
use CE. You can set up CE and just run it when you want it, like other
python add-ons. That might not be the case for the most recent version
thoug
I have no experience with fuse, but my guess would be Mariana might
want to just use 'bond' and translate one termini as needed. If she
doesn't want to "manually" translate, there is always energy
minimization to correct bond lengths.
Take Care.
On Tue, Dec 8, 2009 at 12:59 AM, Nir London wrote:
Saeid,
If you know exactly which atoms in protein A are to be paired with atoms in
protein B, then this is "fitting" and PyMOL can do it with the "fit" family
of commands. In PyMOL type, "help fit" to get help and "fit ?" for fit's
syntax. (A neat trick in PyMOL: "commandName ?" will show you in
Hey Saeid,
use the 'super' command. Type
super protein1, protein2
For more information, check teh wiki.
Andreas
On Tue, Dec 8, 2009 at 7:07 AM, saeid mirzaei wrote:
> Hi everyone,
>
> could some one tell me I can use Pymol for superimposing two protein or not
> if so how can I use it?
>
