VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Oct 09 2015 - 02:56:42 CDT

Hey Atanu,

 

vmd doesn’t calculate the secondary structure itself, so far, instead it created a pdb file and calles an external tool called “stride”,

which is located in the vmd installation folder. You can try to run this tool on your pdb manually and see if it

let you modify the parameters you want from the command line.

 

Norman Geist

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Atanu Maity
Gesendet: Freitag, 9. Oktober 2015 08:44
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: query regarding phi-psi range for asigning secondary structure

 

Dear users,

 

This may be a very general query, but I have searched many previous threads but could not find what are the range used for phi-psi to assign secondary structure.

 

The command "vmd_calculate_structure" follwed by " $atomselection get structure" prints the one letter code ( e. g. T/H/C).

 

I tried to find a source file where the cutoff may be mentioned, but could not find.

 

Can someone help me, at least what should I check to find it.

 

With regards,

 

Atanu Maity

 

Research Scholar

Bioinformatics Center

Bose Institute