Is it really possible in g_hbond to get hbmap.xpm for plotting only those hydrogen bonds between chain A and chain B of protein which has %age existence greater than say 80%.
shahid On Sat, Mar 12, 2016 at 10:25 PM, Justin Lemkul <[email protected]> wrote: > > > On 3/12/16 5:44 AM, tasneem kausar wrote: > >> Dear all >> >> I have plotted the hydrogen bonds present at the interface of protein in >> its binary complex. I have already written the index file for the >> interface >> residues then used it for hydrogen bond calculation. There are a number of >> bonds at the interface. I am trying to put a cut off of 50 % for existence >> of hydrogen bonds in the whole trajectroy. So I want to remove the rest of >> hydrogen bonds of interface residues whose existence is less than 50% . >> For >> this purpose how should I edit the .eps file. Because there are a lot of >> data written and I am not able to understand the data that are given for x >> and y axis. >> Please solve the Issue >> > > An .eps file is an image; I wouldn't advise trying to mess with its > contents to get the information you want. Everything you need should > already be in the normal text output from hbond, most directly the > hbmap.xpm file itself. Parse that information to get what you want. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > [email protected] | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > -- > 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 [email protected]. > -- 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 [email protected].
