Re: [PyMOL] Pymol: Cartoon representation for .pdb file with multible entries

[Robert C. <rob...@qu...>]

Hi Alexander,

On Wed, 2011-10-26 12:53  EDT,  Alexander Schulz
<sc...@dw...> wrote:

> Hi Thomas,
> 
> thank you very much for the answer, I'm beginning to understand the
> actual problem now. 
> 
> dss state=1 
> helps, but it changes the problem: I would like to see the secondary
> structure that corresponds to the single snapshot. When I use dss
> state=1, I just see the secondary structure of the first snapshot in all
> snapshots. 
> 
> Is there a way to calculate the secondary structure for each individual
> snapshot stored in this single .pdb file?

Yes, simply load the pdb file with the "discrete=1" flag:

load md_file.pdb, discrete=1
dss md_file

Setting the "discrete" flag causes PyMOL to store more information
(B-factors, secondary structure) with each atom of each state -- so it can
also be noticeably slower to load and uses more memory.

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc