Paymon Pirzadeh wrote:
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
When prompted for only one group, that group is used for calculation and output.
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?
Yes, use an .m2p file to adjust the matrix spacing. This was discussed several
days ago.
By the way, what would the option -nice do here?
Likely nothing. Nice levels are irrelevant for most tasks.
-Justin
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
========================================
--
========================================
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
========================================
--
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