On 8/15/12 4:54 PM, Andrew DeYoung wrote:
Hi again,
I just looked at page 214 in the version 4.5.4 PDF manual (not the -h man
page), and it says:
"An H-bond existence map can be generated of dimensions # H-bonds X #
frames. The ordering is identical to the index file (see below), but
reversed, meaning that the last triplet in the index file corresponds to the
first row of the existence map."
So this seems to answer my question. The order is indeed reversed. I do
NOT mean this as a criticism, but just politely I would like to say that the
-h man page for g_hbond may thus be a little vague and potentially
misleading.
We've had these discussions before on the list (several times). It may be a bit
confusing at first, but if you think about the numbering of the y-axis in the
.xpm file, it is numbered like any other, starting with the coordinate origin.
Thus the values increase upward. To plot it "backwards" I think would be vastly
more confusing, and each analysis program (g_hbond, do_dssp, g_mdmat, etc) would
have to choose whether its output would be written "forward" or "backward" since
they all share the same code for writing .xpm files.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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