One other thing -
PyMOL has a flag which determines whether the density values will be
normalised - if this flag is not set, then
isomesh mesh_name, map_name, 1
will contour the map at 1-sigma; to contour at an absolute value, you must
do
set normalize_ccp4_maps=0
BEFORE loading the map. If the flag is set, the program will print some
information about the calculated mean and std deviation when you load a
map. Commonly-used settings like this can be put in your ~/.pymolrc file
(at least on a UNIX system), so that they are executed whenever PyMOL
starts up.
Gareth
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Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD [email protected]
Tel 01223 492548 http://www.ebi.ac.uk/~gareth
