[gmx-users] gmx do_dssp

[Bratin Kumar Das]

You can run xpm2ps command to make the .xpm file excitable

On Mon 18 Mar, 2019, 10:58 PM João Henriques <joao.m.a.henriques at gmail.com
wrote:

> Hello Eduardo,
>
> The xpm file contains all the info about axes, keys, etc. Look at this
> excerpt from a random xpm file from one of my simulations:
>
> /* This file can be converted to EPS by the GROMACS program xpm2ps */
> /* title:   "Secondary structure" */
> /* legend:  "" */
> /* x-label: "Time (us)" */
> /* y-label: "Residue" */
> /* type:    "Discrete" */
> static char *gromacs_xpm[] = {
> "50001 69   8 1",
> "~  c #FFFFFF " /* "Coil" */,
> "E  c #FF0000 " /* "B-Sheet" */,
> "B  c #000000 " /* "B-Bridge" */,
> "S  c #008000 " /* "Bend" */,
> "T  c #FFFF00 " /* "Turn" */,
> "H  c #0000FF " /* "A-Helix" */,
> "I  c #800080 " /* "5-Helix" */,
> "G  c #808080 " /* "3-Helix" */,
>
> With a bit of scripting you can turn this xpm file into anything you like.
> Also, I haven't used it yet, but this exists and can perform several
> operations/analyses on xpm files:
> https://github.com/HITS-MBM/conan/blob/master/docs/index.md
>
> Cheers,
> João
>
> On Mon, Mar 18, 2019 at 5:45 PM Eduardo Diniz <dududiniz94 at hotmail.com>
> wrote:
>
> > Hello!
> >
> > I'm wanting to keep track of secondary structure (ss) elements in my
> > protein simulation but I have some questions about the do_dssp tool of
> > gromacs. The two main output files it produces is a ss.xpm file which
> I've
> > found very difficult to interpret, mainly because I don't know what that
> > colors code represent and the x and y axis are not specified (I think
> the x
> > axis is time and the y axis is residue).
> >
> > The second file is the scount.xvg file which indicates the number of
> > residues belonging to one of eight secondary structure elements, but for
> me
> > this information isn't enough, because I want to know what residues
> belong
> > to what ss element.
> >
> > One optinal output file that I think might be useful for me is the
> > ssdump.dat file, which shows (I suppose) what residues belongs to what ss
> > elements, but I don't know what those letters (E, S H etc) means.
> >
> > Sorry if what I ask is stupid. Hope someone can help me. Thanks in
> advance
> > for your time.
> >
> > Eduardo
> > --
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