<div dir="ltr">Hi all experts,<br><br>Can I select all the residue which are lying within a given distance from one residue ?, using any of the tool in pymol, vmd, chimera or gromacs.<br>Whether the option of g_hbond which gives the pair within a particular distance can be used for the same purpose ?, FYI, I am having one pdb entry for the same (no .trr and .tpr).<br>
<br>with thanks,<br>Vivek<br><br><div class="gmail_quote">2008/10/6 Steven Kirk <span dir="ltr"><<a href="mailto:steven.kirk@hv.se">steven.kirk@hv.se</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi there,<br>
<br>
This is the question out of gromacs..but I need it urgently.. and I hope<br>
this is the only place where I can get such expert to solve my query...<br>
while trying to restrict my MDRUN for a particular site of the protein<br>
molecule I want to visualize the site and find out the centroid for the<br>
particular site......<br>
<br>
Is there any visualization tool that can do the same ..<br>
I mean Is there any molecular visualization tool that can help in finding<br>
out the ...centroid between a group of resuidues ?<br>
</blockquote>
<br></div>
Pymol has a script that computes the center of mass for a selection, and optionally, moves this center of mass to the origin:<br>
<br>
<a href="http://pymolwiki.org/index.php/COM" target="_blank">http://pymolwiki.org/index.php/COM</a><br>
<br>
Haven't used it myself, so I can't vouch for its effectiveness.<br>
<br>
Steve Kirk<br><font color="#888888">
-- <br>
Dr. Steven R. Kirk <<a href="mailto:steven.kirk@hv.se" target="_blank">steven.kirk@hv.se</a>, <a href="mailto:S.R.Kirk@physics.org" target="_blank">S.R.Kirk@physics.org</a>><br>
Dept. of Technology, Mathematics & Computer Science (P)+46 520 223215<br>
University West (F)+46 520 223299<br>
Trollhattan 461 86 SWEDEN <a href="http://beacon.webhop.org" target="_blank">http://beacon.webhop.org</a></font><div><div></div><div class="Wj3C7c"><br>
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