VMD-L Mailing List
From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Oct 09 2015 - 05:29:00 CDT
Maybe the report.C contains to the external stride tool?
What exactly do you try to find out or what are you trying to accomplish?
Von: Atanu Maity [mailto:atanuchem48_at_gmail.com]
Gesendet: Freitag, 9. Oktober 2015 11:44
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Betreff: Re: vmd-l: query regarding phi-psi range for asigning secondary structure
Thank you Norman for your help.
I have gone through the 'Stride.c' and found that it actually processes the output line from another source called 'Report.c' as written in the file ----
/* Here's the sprintf command stride uses on output in report.c:
00081 sprintf(Tmp,"ASG %3s %c %4s %4d %c %11s %7.2f %7.2f %7.1f",
00086 Here's a typical line:
00087 ASG THR - 9 9 B Bridge -113.85 157.34 21.9 ~~~~
I searched for Report.c but it is not there in the repository.
Tnaks in advance.
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.
Von: owner-vmd-l_at_ks.uiuc.edu <mailto:owner-vmd-l_at_ks.uiuc.edu> [mailto: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 <mailto:vmd-l_at_ks.uiuc.edu>
Betreff: vmd-l: query regarding phi-psi range for asigning secondary structure
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.