VMD-L Mailing List

From: aneesh cna (aneeshcna_at_gmail.com)
Date: Mon Aug 13 2007 - 05:31:32 CDT

Hello VMD users,
           i would like to use STRIDE for evaluating the secondary
structural chages in particular region in my protein over a time interval.
I searched the net for getting an idea about the way how srtide will use
with vmd but i cant found out related web pages. can you help me in this
matter?

 I installed STRIDE source codes with VMD and when i typing stride in the
terminal it shows

   Action: secondary structure assignment
Usage: stride [Options] InputFile [ > file ]
Options:
  -fFile Output file
  -mFile MolScript file
  -o Report secondary structure summary Only
  -h Report Hydrogen bonds
  -rId1Id2.. Read only chains Id1, Id2 ...
  -cId1Id2.. Process only Chains Id1, Id2 ...
  -q[File] Generate SeQuence file in FASTA format and die
 Options are position and case insensitive

In what way i have to specify the commands? Hope you will help me in this
matter

yours faithfully
Aneesh