You can run xpm2ps command to make the .xpm file excitable On Mon 18 Mar, 2019, 10:58 PM João Henriques <joao.m.a.henriq...@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 <dududini...@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 > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.