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:
- Number of subunits displayed from multimeric complexes.
- presence and number of bound ligands, number of water molecules, ions,
etc.
- resolution, literature references,
- specific mention of which PyMOL display commands access which type of data
Those of us who are trying to teach ourselves this stuff are bewildered by
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).
- 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
