[gmx-users] gmx do_dssp

[João Henriques]

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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