[PyMOL] Re: PyMOL-manual

[<wg...@ch...>]

On Tuesday, December 24, 2002, at 12:07 PM, 
pym...@li... wrote:

>    1. Suggestions for manual - nonspecialists perspective (James L. 
> Kilgore)
>
>
> What I'd like to see written in an accessible form for a 
> non-programmer is
>
> 1) A concise-but-ground-up description of what information is in a PDB
> file and other file formats including:

http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
>
>  2)  How to read the file documentation from within PyMOL:
>
> - Go over the conventions for annotating structure files or at least
> link to something LESS THAN 300 PAGES LONG that explains the salient
> points).

http://pymol.sourceforge.net/html/toc.html

http://www.rubor.de/bioinf/pymol_tips.html

http://tofu.tamu.edu/pymol/

http://pymol_tutorial.tripod.com/

> - How to display protein sequence, including disulfide bond positions
> -  conditions for determination (e.g. low pH often used in NMR, could
> affect structure).
>
> 3) Directions on how to select and alter display parameters for 
> entities
> by connection like bound ligands, a selected number of contiguous
> polypeptide residues or one of several subunits, etc.
>
> 4) Instructions on options to selectively visualize interfaces between
> molecules.
>
> 5) Description and display of calculated features like electrostatic
> surfaces, hydrogen bond locations, etc.
>
> One possibility for making the software more user-friendly would be to
> organize a user  "Quick Start" abbreviated file containing links to the
> main document.
>
> -- 
> Jim Kilgore
>
>
>
>
>
>
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>
William G. Scott

Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

phone:  +1-831-459-5367 (office)
                +1-831-459-5292 (lab)
fax:         +1-831-4593139  (fax)