From: Axel Kohlmeyer (
Date: Tue Dec 14 2010 - 02:33:54 CST

2010/12/14 JhonY. I. <>:
> I know that B factor of pdb file can be shown as color in VMD.
> By the way, can I load information on B factor as indepdent data file for a
> certain pdb file?

actually, using the b-factor field in pdb files is a crutch
and only works globally, i.e. cannot be used for timestep
specific data. a better location is the user field. to load
data into that field, you have to use tcl scripting. you use
standard tcl scripting to read a file. create an atom selection
and then assign it to the user (or user2, user3, or user4) field.
this is documented in the vmd user's guide and some additional
examples are in the vmd script tutorials and in:

> Otherwise, is there no way except for making pdb file appropriate to it?
> Best regards,
>   Luke

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.