[gmx-users] Extraction of the pdb data from the g_shame diagrams

Justin Lemkul jalemkul at vt.edu
Wed Apr 22 14:14:59 CEST 2015

On 4/21/15 1:24 PM, James Starlight wrote:
> and what the most trivial way to find correspondence of the line in
> the data file to what I actually see on the its graph (projection)  ?
> Sorry I'm not an expert of xmgrace so it might seems for you trivial
> :)

It's nothing to do with XmGrace.  The g_sham surface is a 2-D histogram.  If you 
identify a spot on the surface that is of interest, you have some window of 
values into which the PCs fall.  Parse your data file (the one you input into 
g_sham) with any script you like (trivial with Perl, Python, etc) for values in 
that range and print out the line number.  That frame should correspond to a 
member of that histogram on the surface.



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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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