Also you can use
load A.pdb B.pdb C.pdb
or load *pdb
leila karami wrote:
Dear all
very thanks for your time and attention.
my problem was solved by
load A.pdb
load B.pdb
I made a mistake. I meant command-line
pymol *pdb or pymol A.pdb B.pdb
etc. Not load *pdb.
Maia Cherney wrote:
Also you can use
load A.pdb B.pdb C.pdb
or load *pdb
leila karami wrote:
Dear all
very thanks for your time and attention.
my problem was solved by
load A.pdb
load
Thanks, Zhijian
It worked
zjxu wrote:
Dear Maia,
Would you like to try this:
select bridge, (c. a and i. 160+356+505+507+508) or (c. c and i.
275+355+128)
Best Regards,
Zhijian Xu
Maia Cherney wrote:
Hi Jason,
I keep sending my e-mail from a wrong address that the pymol mailing
Hi Jason,
I keep sending my e-mail from a wrong address that the pymol mailing
list does nor recognize.
I need a command that would allow me to select several residues from two
chains, something like that:
select bridge, /prot//A/160+356+505+507+508/+prot/C//275+355+128/
But I cannot find
Hi,
Can anybody advise me what is the right command for selecting or
coloring many hbs?
Instead of
color black, hb1
color black, hb2
etc
I want something like color black, hb1+hb2+hb3 etc.
Maia
--
Colocation vs.
Hi Jason,
I generated hbs from mode=2 method. It made some wrong hbs. How can I
delete those wrong hbs?
Maia
--
Colocation vs. Managed Hosting
A question and answer guide to determining the best fit
for your
For me,
color red, resn asp+glu
works.
Maia
Martin Hediger wrote:
Dear all
What is the selection syntax to select all GLU and ASP residues within
an object?
I'm trying it the way its written on the wiki:
remove resn hoh# remove water
h_add # add hydrogens
as
Program Vasco can do it.
Sebastian Kruggel wrote:
dear all,
i am looking for a possibility to map lipophilic potential
on pymol generated surfaces. i didn't find anything in the
documentation and in the mailing list the question came up once
and PyMOL are you using?
Cheers,
-- Jason
On Wed, Jun 2, 2010 at 10:52 AM, Maia Cherney ch...@ualberta.ca wrote:
I had once a problem with pymol that itr would not open from a terminal
window. After a long battle with it, the problem was solved after I
upgraded my OS.
Robin Emig wrote
I had once a problem with pymol that itr would not open from a terminal
window. After a long battle with it, the problem was solved after I
upgraded my OS.
Robin Emig wrote:
Does anyone else have the problem where pymol dies, or wont update the
display after minimizing on windows? Is there
I would like to show coordination bonds between Mg ion and its ligands
(oxygens) as broken lines, the distance of Mg-O bond is between 1.9-2.2 A.
Maia
--
___
PyMOL-users
Docking is very non-reliable.
E. Krissinel (2009). /Crystal contacts as nature's docking solutions/.
J. Comp. Chem., in press; published on-line 6 May 2009; DOI
10.1002/jcc.21303
Maia
humayun scherrif wrote:
Hello,
Thank you for detailed explanation, surely it is helping me to sort
out
Thank, Robert, Jason.
Finally I figured this out with your help.
Maia
Robert Campbell wrote:
Hi Maia,
Just to add to what Jason said:
On Thu, 22 Apr 2010 17:16:41 -0400, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
2. Which plugin allows me to move one structure relative to
/pymol/__init__.py:sys.path.append(freemol_libpy)
Hopefully this all helps.
-David
- Original Message
From: Maia Cherney ch...@ualberta.ca
To: Jason Vertrees jason.vertr...@schrodinger.com
Cc: pymol-users@lists.sourceforge.net
Sent: Wed, January 20, 2010 9:37
, Maia Cherney ch...@ualberta.ca wrote:
Hi Jason
I need such features. I open two different pdbs and I want to manually move
one structure relative to another. I want to dock one structure into another
or superpose 2 structures manually. Is it possible?
Or I want to move a fragment
Hi Jason
I need such features. I open two different pdbs and I want to manually
move one structure relative to another. I want to dock one structure
into another or superpose 2 structures manually. Is it possible?
Or I want to move a fragment of the molecule relative to the rest of the
molecule cleanup and editing.
Try putting your mouse into Editing Mode and moving atoms around.
It's not hard. Check this out:
http://pymolwiki.org/index.php/Molecular_Sculpting for some help.
Regards,
-- Jason
On Wed, Jan 20, 2010 at 11:52 AM, Maia Cherney ch...@ualberta.ca wrote
Hi John,
I have a similar problem with my ubuntu 8.10. When I use a command
window, I get the error message:
Traceback (most recent call last):
File /var/lib/python-support/python2.5/pymol//__init__.py, line 167,
in module
import pymol
File
Hi,
Is it posible in pymol to select all residues of a certain type
automatically, like all arginines or all lysines + arginines in a chain?
Maia
--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008
Hi,
Could you please help me with a pymol problem. I have ubuntu linux and I
have pymol in the /usr/bin (comes with ubuntu installation) and also one
in the /programs/linux directory. But I can't open pymol in a terminal
(both installations), only from applications/education menu. I get this
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