[ccp4bb] Pymol questions

2011-05-04 Thread jlliu liu 
Hi All,

I have two questions for Pymol.

1. Can you write out the PDB file after structural alignment?
2. How to only show structure that is several angstrom from the ligand?

Thanks a lot in advance!

Eric

Re: [ccp4bb] Pymol questions

2011-05-04 Thread Matthew Chu 
1. Yes, just Save Molecule (individually) after align

2.  show stick, HETATM around 4
( is your pdb name, 4 = 4 angstrom)



On Wed, May 4, 2011 at 3:26 PM, jlliu liu jlliu20022...@gmail.com wrote:

 Hi All,

 I have two questions for Pymol.

 1. Can you write out the PDB file after structural alignment?
 2. How to only show structure that is several angstrom from the ligand?

 Thanks a lot in advance!

 Eric




-- 

Matthew L.H. Chu, PhD
Postdoctoral Scholar - Weis Lab
Department of Structural Biology
Stanford School of Medicine

Re: [ccp4bb] Pymol questions

2011-05-04 Thread Eric Larson 

Hi Eric,

On Wed, 4 May 2011, jlliu liu wrote:


Hi All,

I have two questions for Pymol.


the pymol wiki is your friend (http://www.pymolwiki.org/index.php/Main_Page)

as is the pymol users mailing list 
(http://sourceforge.net/mail/?group_id=4546).  Follow the link to subscribe.



1. Can you write out the PDB file after structural alignment?


yes you can (http://www.pymolwiki.org/index.php/Save)


2. How to only show structure that is several angstrom from the ligand?


use the selection algebra rules 
(http://www.pymolwiki.org/index.php/Selection_Algebra)

happy pymoling,

Eric



Thanks a lot in advance!

Eric





Eric T. Larson, PhD
Biomolecular Structure Center
Department of Biochemistry
Box 357742
University of Washington
Seattle, WA 98195

email: larso...@u.washington.edu