[gmx-users] DSSP => how to edit .eps file
David van der Spoel
spoel at xray.bmc.uu.se
Sat Apr 3 21:29:35 CEST 2010
On 4/3/10 9:19 PM, Justin A. Lemkul wrote:
> Chih-Ying Lin wrote:
>> HI After running DSSP, .eps files are created.
> No they aren't; you create .eps files from the .xpm output that do_dssp
>> We can see the second structures of the all residues.
>> I only want to see the change of the second structures of some
>> specific residues.
>> How can i do it?
> As with most (all) Gromacs analysis tools, create an index group for the
> residues you want to analyze. That will require you to re-run your
> analysis or otherwise hack your .xpm file (probably not a good idea).
>> Also, how can I change the thickness of the color band for each residue?
> Use an appropriate .m2p file to alter the attributes of the data. An
> example is given in the online manual.
>> The logo indicates the color of different second structure is shown
>> not clear for me, how can i make the change on it?
> Do you want to change the colors assigned, or some other aspect of the
> legend? You could, in theory, edit the color assignments in the .xpm file.
With the option
-sss string HE
you can also choose to show only helix and sheet
>> Thank you
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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