You calculate rmsf of both proteins separately and then plot them together and look the region of your interest...... <br><br><div class="gmail_quote">On Wed, Feb 9, 2011 at 10:28, bharat gupta <span dir="ltr"><<a href="mailto:bharat.85.monu@gmail.com">bharat.85.monu@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">I used the -res option ... and I got the rmsf in terms of residues but still the problem is that the two structures contain different amount of residues due to loop replacement in one structure.. In that case how shall proceed to check the effect of loop insertion on the overall topology of the protein.. pls guide ??<div>
<div></div><div class="h5"><br>
<br><div class="gmail_quote">On Tue, Feb 8, 2011 at 7:21 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><br>
<br>
bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Actually after loop incorporation I want to check which region of the protein shows much deviation , which I think can be done by plotting rmsf values from both proteins.. but the problem here is that one structure which contains loops has more no. of atoms as compared to other str. without loop insertion .. so which way it can be analyzed ??<br>
<br>
Also g_rmsf gives RMSF values for atoms of residues but not of residues how can I get the values for residues .. <br>
</blockquote>
<br></div>
Please read g_rmsf -h.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Pls help ??<div><div></div><div><br>
<br>
On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
bharat gupta wrote:<br>
<br>
Hi,<br>
<br>
I want to calculate the RMSF of residues and not of protein ...<br>
how can this be done with g_rmsf..<br>
<br>
Also I want to see the rmsf of certain residues .. for which I<br>
created the .ndx file containint those residues only .. and<br>
after using g_rmsf with index file gives the RMSF for whole<br>
protein backbone and not for that index file residues ... what<br>
shall I do to have RMSF of index file residues ??<br>
<br>
<br>
The default output of g_rmsf is a plot of RMSF (of each residue) vs.<br>
residue. No index file is required to obtain this, unless you want<br>
to do the fitting to some custom group. Is this not what you want?<br>
<br>
-Justin<br>
<br>
-- Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
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Virginia Tech<br>
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-- <br>
Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
Biomolecular Engineering Laboratory<br>
Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>
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South Korea<br>
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========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>
Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>
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---------------------------------<br>Thanks and regards<br></div><div><span style="font-family: arial; font-style: normal;"><i><font face="arial, helvetica, sans-serif">Bipin Singh</font></i></span></div></font></i></font><div>
<font color="#3333ff" face="arial, helvetica, sans-serif"><i><br></i></font></div><br>