Dear Sir, <br><br>I tried fitting the proteins of the trajectory in pymol <br>as mentioned in your (Dr. Tsjerk's) tutorial, but later<br>I tried using the trjconv -fit rot+trans to fit the proteins<br>in the trajectory as you had mentioned. <br>
<br>I do not observe this degree of movement in protein<br>when I view the trajectory along any 1-5 eigen vectors.<br>This trajectory along any of these eigen vector is very minute<br>and cannot be compared to that obtained after superposing<br>
the structure in the trajectory. Why is it so?<br>Please let me know if I am understanding the concept wrong.<br><br>Thanking you<br>With regards<br>M. Kavyashree<br><br><br><div class="gmail_quote">On Thu, Jun 23, 2011 at 11:56 AM, Kavyashree M <span dir="ltr"><<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Thank you Sir!<br><br>With regards<br><font color="#888888">M. Kavyashree</font><div><div></div><div class="h5"><br><br>
<div class="gmail_quote">On Thu, Jun 23, 2011 at 11:50 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p>trjconv -fit rot+trans</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p></p><blockquote type="cite"><div>On Jun 23, 2011 8:12 AM, "Kavyashree M" <<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a>> wrote:<br><br>Dear Users, <br><br>Are there any tool for superposing the trajectory <br>
structures form MD. Please correct me if I am asking<br>any illogical question.<br>My previous question was regarding the trjconv output<br>pdb trajectory, is there a way to superpose all these <br>
structures?<br><br>Thank you<br>With regards<br><font color="#888888">M. Kavyashree <br></font></div><p><font color="#500050">
On Wed, Jun 22, 2011 at 10:52 PM, Kavyashree M <<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a>> wrote:
>
> Dear users,
>
> I...</font></p><br>--<br>
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