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Hi,<br>
<br>
The -ins option is badly broken as far as I know. Don't expect it to
work anytime soon.<br>
<br>
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.<br>
<br>
Cheers,<br>
<br>
Erik<br>
<br>
leila karami skrev 2010-11-24 16.07:
<blockquote
cite="mid:AANLkTikmOxojWNbFFpcSBZYWmbezjZnJJWVSeGjHoEnj@mail.gmail.com"
type="cite"><span style="font-family: arial,helvetica,sans-serif;">Dear
Erik and Justin</span><br>
<br>
Thank you so much for ypur help.<br style="font-family:
arial,helvetica,sans-serif;">
<br style="font-family: arial,helvetica,sans-serif;">
<span style="font-family: arial,helvetica,sans-serif;">yes I mean
water mediated hydrogen bonds (protein-H2O-dna)</span>.<br>
<br>
since I'm beginner in perl script, please clarify your answer and
explain more. what is your mean of <br>
existence functions exactly?<br>
<br>
do using of -ins option in g_hbond tool help me?<br
style="font-family: arial,helvetica,sans-serif;">
<br style="font-family: arial,helvetica,sans-serif;" clear="all">
<br>
-- <br>
<pre style="font-family: arial,helvetica,sans-serif;">Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group</pre>
<br>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
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
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
</pre>
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