Hi Elaine,<br><br>Many thanks for the detailed information! I have managed to use matchmaker and save the RMSD values as you described in method (A), but the problem is that MultialignViewer measures only the RMSD of the CA atoms that were used in the alignment. In my case I want to align chains B of the two structures but measure the RMSD between chains A. Is it possible to do that?<br>
<br><br>Thanks in advance for any help.<br><br>Thomas<br><br><br><div class="gmail_quote">On 3 April 2012 19:36, Elaine Meng <span dir="ltr"><<a href="mailto:meng@cgl.ucsf.edu">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">Hi Thomas,<br>
Two general possibilities:<br>
<br>
(A) If the RMSD is to be calculated by Chimera, you would need to superimpose the proteins to calculate the RMSD, then color by that value using Render by Attribute or command rangecolor. However, after the coloring step you could move the proteins apart. The RMSD calculation in Chimera uses CA atoms, so if you only have two proteins, the per-residue "RMSD" boils down to simply the CA-CA distance between the two proteins in the superimposed state.<br>
<br>
<<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers</a>><br>
<<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render</a>><br>
<<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html</a>><br>
<br>
(B) Alternatively, if the RMSD is calculated by some other program you could create an "attribute definition" file that lists the values, read the file into Chimera to assign the attribute values to residues (or atoms), and then color by your custom attribute the same way as in (A). The attribute file format is quite simple, see description and examples:<br>
<<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile</a>><br>
<br>
However, method (A) is probably easiest if the CA-CA distance is an acceptable measure. Example using MatchMaker command (mm) to superimpose and show sequence alignment:<br>
<br>
open 2gbp<br>
open 2fw0<br>
mm #0 #1 show true<br>
... sequence alignment should appear, including RMSD histogram above the sequences ...<br>
<<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html</a>><br>
<br>
To define and apply the coloring, you could use Render by Attribute (see the attribute of residues named mavRMSD) or rangecolor, for example:<br>
<br>
rangecolor mavRMSD min purple mid red max yellow<br>
<br>
Then you can un-superimpose the structures, for example, with command: reset, or manually with the mouse.<br>
<<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef</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></div><div class="h5"><br>
<br>
<br>
On Apr 3, 2012, at 5:46 AM, Thomas Evangelidis wrote:<br>
<br>
> Dear UCSF Chimera users and developers,<br>
> Is it possible to color a pair of structures representing different stages of the thermodynamic cycle of a protein by the RMSD, without aligning them?<br>
> thanks in advance,<br>
> Thomas<br>
<br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>
<p style="margin-bottom:0cm" align="LEFT">======================================================================</p>
<p style="margin-bottom:0cm" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom:0cm" align="LEFT">PhD student</p>
<p style="margin-bottom:0cm" align="LEFT">Biomedical Research
Foundation, Academy of Athens</p>
<p style="margin-bottom:0cm" align="LEFT">4 Soranou Ephessiou , 115 27
Athens, Greece<br><br>email: <a href="mailto:tevang@bioacademy.gr" target="_blank">tevang@bioacademy.gr</a></p>
<p style="margin-bottom:0cm" align="LEFT"> <a href="mailto:tevang3@gmail.com" target="_blank">tevang3@gmail.com</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>
</p>
<br>