VMD-L Mailing List

From: Jim Pfaendtner (jpfaendt_at_hec.utah.edu)
Date: Thu Aug 09 2007 - 16:49:58 CDT

Hi,

I have used CHARMM to build a complex of several proteins and the new
proteins do not show secondary structure in VMD when I try to draw
them with "ribbons or new cartoon". I noticed that the input pdb
file has values for temperature factor (2.0 for H atoms and 5.0 for
heavy atoms) whereas my new CHARMM output pdb file has all zeros for
the temperature factor (column 63 in my pdb file).

Could this be the reason Stride is not drawing the same secondary
structure?

Is there an easy way to generate the temperature factors using CHARMM
or psfgen?

Thank you,
Jim