From: Atanu Maity (atanuchem48_at_gmail.com)
Date: Fri Oct 09 2015 - 04:44:24 CDT

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:
00080
00081 sprintf(Tmp,"ASG %3s %c %4s %4d %c %11s %7.2f
%7.2f %7.1f",
00082 p->ResType,SpaceToDash(Chain[Cn]->Id),p->PDB_ResNumb,i+1,
00083 p->Prop->Asn,Translate(p->Prop->Asn),p->Prop->Phi,
00084 p->Prop->Psi,p->Prop->Solv);
00085
00086 Here's a typical line:
00087 ASG THR - 9 9 B Bridge -113.85 157.34
21.9 ~~~~
00088
00089 */

I searched for Report.c but it is not there in the repository.

Tnaks in advance.

On Fri, Oct 9, 2015 at 1:26 PM, Norman Geist <norman.geist_at_uni-greifswald.de
> wrote:

> 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
>