[gmx-users] make_ndx for do_dssp

[Paymon Pirzadeh]

I assumption was that when provide the index file, do_dssp will do the
analysis for the protein but prints out the results only for the
designated residues. All I wanted was a better resolution on the final
xpm plot to see the secondary structure of the protein at those residues
of interest. Any suggestions on how we can increase the resolution of
dssp plot and enlarging the axis of residues?
By the way, what would the option -nice do here?

Paymon 


On Wed, 2010-10-06 at 15:29 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > Justin,
> > I produced the index file based on your suggestion, but when I ran the
> > do_dssp, a completely different result was spit out comparing to what
> > the whole protein analysis had given. Any ideas on why that might have
> > happened?
> > 
> 
> That depends on what "completely different" means.  I have no idea.  If you're 
> only analyzing a subset of the residues, you're going to get a discontinuous 
> plot that's probably going to look a whole lot different from any analysis done 
> on the whole protein.  What's more, if you're only considering small fragments 
> of the protein, then omitting surrounding residues from the analysis probably 
> won't permit DSSP to find hydrogen bonding partners that are necessary to 
> determine the correct secondary structure.
> 
> -Justin
> 
> > Paymon
> > 
> > On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> Hello, I want to check the secondary structure of protein at particular
> >>> residues. Since dssp needs all main chain atoms, does the following command
> >>> at the make_ndx prompt makes the correct index file? 
> >> You can answer that yourself by looking at the resulting index file.
> >>
> >>> 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45
> >>>
> >> To get these groups to merge, I think you probably need to do 5 & r 1 | ...
> >>
> >> -Justin
> >>
> >>> (Main chain atom of particular residues). regards,
> >>>
> >>> Paymon
> >>>
> >> -- 
> >> ========================================
> >>
> >> Justin A. Lemkul
> >> Ph.D. Candidate
> >> ICTAS Doctoral Scholar
> >> MILES-IGERT Trainee
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >> ========================================
> > 
> > 
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================