Re: [PyMOL] how to load two separate pdb files simultaneously

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

Re: [PyMOL] how to load two separate pdb files simultaneously

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

Re: [PyMOL] [Fwd: Re: select residues from different chains]

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

[PyMOL] [Fwd: Re: select residues from different chains]

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

Re: [PyMOL] hbs

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.

Re: [PyMOL] delete an hb from a multiple hb object

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

Re: [PyMOL] Selecting ASP and GLU

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

Re: [PyMOL] map lipophilic potential

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

Re: [PyMOL] pymol dies when minimizing

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

Re: [PyMOL] pymol dies when minimizing

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

Re: [PyMOL] coordination bonds

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

[PyMOL] [Fwd: Re: Symmetry Mates Problem]

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

Re: [PyMOL] PyMOL Plugin Architecture

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

Re: [PyMOL] pymol and freemol

/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

Re: [PyMOL] new ideas

, 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

Re: [PyMOL] new ideas

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

Re: [PyMOL] new ideas

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

Re: [PyMOL] [Solved] Upgraded computer, Pymol usable again. :^)

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

Re: [PyMOL] Alignment Objects

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

[PyMOL] pymol does not open from a terminal

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