Changes between Initial Version and Version 1 of ChIMP/MultiFit


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Timestamp:
Mar 17, 2009, 2:20:22 PM (17 years ago)
Author:
goddard
Comment:

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  • ChIMP/MultiFit

    v1 v1  
     1{{{
     2#!html
     3
     4<h1>Fitting in EM map with MultiFit and Chimera</h1>
     5
     6<p>
     7Keren Lasker<br>
     8Tom Goddard<br>
     9February 23, 2009
     10</p>
     11
     12<p>
     13Illustration of fitting atomic models into EM map using MultiFit from Sali lab
     14in combination with Chimera.
     15
     16</p>
     17
     18<ul>
     19<li>Graph calculated for map using k-means, one node per protein.
     20<li>Proteins hand placed at presumed locations.
     21<li>Optimize placements using MultiFit, handles steric clashes.
     22</ul>
     23
     24<p>
     25Other cases allow specifying restraints for which proteins contact which others and
     26for allowing MultiFit to determine best protein locations on graph.
     27</p>
     28
     29<table cellspacing=10>
     30<tr>
     31<td><img src="1z5s_9A.png" height=350>
     32<td><img src="1z5s_graph.png" height=350>
     33<td><img src="1z5s_pieces.png" height=350>
     34
     35<tr>
     36<td>4 protein nuclear pore targeting complex (simulated map 9 A from 1z5s).
     37<td>Graph partition of map using k-means algorithm.
     38<td>Crystal structures for fitting into map.
     39<tr>
     40<td><img src="1z5s_place.png" height=350>
     41<td><img src="1z5s_fit.png" height=350>
     42<tr>
     43<td>Hand-placed proteins are associated with closest graph nodes.
     44<td>Computational optimization by MultiFit program.
     45</table>
     46
     47}}}