Re: [modeller_usage] About the Modeller output in PDB format

[Modeller Caretaker <modeller-care@ucsf.edu>]

Yun He wrote:
> Hi, everybody. The structures produced by MODELLER are stored in PDB format, 
> what does the value in last column stand for? In a normal PDB file, there is 
> a temperature factor column, but in the modeller structure, it is not like a 
> temperature factor, what is it?

Normally in an automodel run, model.energy() is called with output='LONG 
VIOLATIONS_PROFILE'. This writes out the per-residue violations of all 
restraints into a .V file, and also into the temperature factor (Biso) 
column of your PDB. See http://salilab.org/modeller/manual/node151.html

You can also call model.write_data() to calculate other properties and 
write them into the Biso column. See 
http://salilab.org/modeller/manual/node141.html

	Ben Webb, Modeller Caretaker
--
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage