Hi,
The -ins option is badly broken as far as I know. Don't expect it to
work anytime soon.
The hbmap.xpm depicts the existence functions h for all hydrogen bonds
as functuions of time. A red pixel means that the hydrogen bond is there
(h=1), white means that the hbond is broken (h=0). If you multiply h(t)
for a certain water molecule interacting with protein with h(t) for the
same water molecule interacting with DNA, then theresulting existence
function will be unity only at those frames where the water hbonds to
both protein and DNA. If you do that for all waters and store the
resulting existence functions in xpm-format you can run Justin's script
on your new data. You need to create a corresponding index file too of
course.
Cheers,
Erik
leila karami skrev 2010-11-24 16.07:
Dear Erik and Justin
Thank you so much for ypur help.
yes I mean water mediated hydrogen bonds (protein-H2O-dna).
since I'm beginner in perl script, please clarify your answer and
explain more. what is your mean of
existence functions exactly?
do using of -ins option in g_hbond tool help me?
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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