VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Oct 12 2015 - 01:44:23 CDT

I guess you might find this information easier querying for ramachandran plot, which defines specific areas as helix or beta.

 

 <http://www.sciencedirect.com/science/article/pii/S0022283663800236> http://www.sciencedirect.com/science/article/pii/S0022283663800236

 

Is contains a picture with an illustration of the angle boundaries.

 

Norman Geist

 

Von: Atanu Maity [mailto:atanuchem48_at_gmail.com]
Gesendet: Montag, 12. Oktober 2015 07:58
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Betreff: Re: vmd-l: query regarding phi-psi range for asigning secondary structure

 

Thank you sir. I have found report.C in the source file of STRIDE.

 

Actually I was trying to calculate percentage of helicity of a peptide during simulation. That I have calculated by processing the secondary structure analysis output file obtained from vmd. Now when I will be using the data an obvious query will be what are the range of phi-psi used for considering helix? That is why I am interested to know about the ranges.

 

Usually phi psi varying in the range (-45 to -60) is considered for alpha helix.

 

Thanks,

Atanu

 

 

On Fri, Oct 9, 2015 at 3:59 PM, Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> > wrote:

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?

 

Norman Geist

 

Von: Atanu Maity [mailto:atanuchem48_at_gmail.com <mailto:atanuchem48_at_gmail.com> ]
Gesendet: Freitag, 9. Oktober 2015 11:44
An: Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> >
Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu <mailto: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:
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> [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

 

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