On Tuesday, December 24, 2002, at 12:07 PM,
pymol-users-requ...@lists.sourceforge.net 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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