Dear Elaine,<div> I am stuck with a new problem and that is can I select multiple </div><div>residues from different chains and check their interaction. There are some results from Haddock and I want to study the interaction residues from different chains. Is it also possible to know their bonding pattern? Please help me out.<br>
<br><div class="gmail_quote">On Thu, Oct 25, 2012 at 9:53 AM, Amit Jaiswal <span dir="ltr"><<a href="mailto:amitjai20@gmail.com" target="_blank">amitjai20@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Elaine,<div><br><div> Thanks for your mail and suggestions. I will post questions </div><div>on <a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a> from next time on wards. I will try the tips and thus report you if problem persists.</div>
<div><br></div><div>With kind regards,</div><div>Amit Jaiswal,</div><div>Pondicherry University,</div><div>Pondicherry,</div><div>India.<div><div class="h5"><br><br><div class="gmail_quote">On Wed, Oct 24, 2012 at 10:03 PM, Elaine Meng <span dir="ltr"><<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Amit,<br>
You can identify hydrogen bonds with FindHBond (in menu under Tools... Structure Analysis). Click the Help button on that tool or see here for instructions:<br>
<<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html</a>><br>
<br>
If you want to analyze the environment around the metal and then add metal coordination bonds, you could use Metal Geometry (in menu under Tools... Structure Analysis):<br>
<<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/metalgeom/metalgeom.html" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/metalgeom/metalgeom.html</a>><br>
<br>
If you don't care about analysis and just want to draw a line between two atoms, you could do that using either of the following:<br>
(A) distance measurements, for example using the Distances tool (change label to "none" if you don't want to see the distance value)<br>
<<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances</a>><br>
(B) PseudoBond Reader<br>
<<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html</a>><br>
<br>
Please send Chimera questions to the <a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a> address so that everybody can benefit.<br>
<br>
You can search the manual using Help... Search Documentation in the Chimera menu, and you can search the chimera-users messages here:<br>
<<a href="http://www.cgl.ucsf.edu/chimera/docs/feedback.html" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/feedback.html</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<div><div><br>
On Oct 24, 2012, at 8:54 AM, Amit Jaiswal wrote:<br>
<br>
> Dear Dr.Meng,<br>
> Many thanks for your mail and suggestion for Metal fixation. I have done what you have advised. So, now my metal is near the catalytic site. So the next step is to form bond between Mg and Aspartic Acid residues. Now, I am confused. So I want to ask weather hydrogen bond and co-ordinate bond can be formed in Chimera?<br>
> Please do let me know.<br>
><br>
<br>
</div></div></blockquote></div><br><br clear="all"><div><br></div></div></div><div class="im">-- <br><br><div>Yours Sincerely,</div><div><br></div><div>~~~~~~~~~~~~~~~~~~~~~~~~</div><div>Amit Jaiswal,</div><div>Department of Bioinformatics,</div>
<div>
School of Life Sciences,</div><div>Pondicherry Central University,</div><div>Kalapet, Pondicherry,</div><div>Puducherry - <span style="background-color:rgb(236,236,236);color:rgb(0,0,128);font-family:Verdana,arial,helvetica,sans-serif;font-size:12px;text-align:justify">605 014.</span></div>
<div>Phone No.: +91 8124954834.</div><div> </div><div>~~~~~~~~~~~~~~~~~~~~~~~~~</div><br>
</div></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><br><div>Yours Sincerely,</div><div><br></div><div>~~~~~~~~~~~~~~~~~~~~~~~~</div><div>Amit Jaiswal,</div><div>Department of Bioinformatics,</div><div>School of Life Sciences,</div>
<div>Pondicherry Central University,</div><div>Kalapet, Pondicherry,</div><div>Puducherry - <span style="background-color:rgb(236,236,236);color:rgb(0,0,128);font-family:Verdana,arial,helvetica,sans-serif;font-size:12px;text-align:justify">605 014.</span></div>
<div>Phone No.: +91 8124954834.</div><div> </div><div>~~~~~~~~~~~~~~~~~~~~~~~~~</div><br>
</div>