| Quick navigation: | Home | Site Map || References | Biography || Copyright | Other copyright | Contact us | | |
|
|
[ccp4bb] Superimposing maps from different crystal forms - solved |
|
CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 29 April 2007Subject: Superimposing maps from different crystal forms - solved From: Andrew Robinson arobinso {- at -} CBMS {- dot -} MQ {- dot -} EDU {- dot -} AU Date: 2007-04-29 Gerard - MAVE worked nicely ... once I remembered how to get data blocks out of O. A summary for the future: I wanted to superimpose electron density maps from two crystal forms of a protein; the apo protein (P43212) and a crystal into which substrate was soaked (P41212). Then I wanted to subtract the apo map from the ligand map, hoping to see density for the ligand. I went about this process as follows: 1) Working with the coordinates in O, I transformed the apo form onto the substrate-containing form and wrote out the transformation matrix. 2) Using MAVE, I "EZ Skewed" the apo map onto the substrate-containing map with the transformation matrix from O. 3) I wrote the map out in P1 with a cubic unit cell 4) In order to put the substrate-containing map into a similar cell, I then repeated the process with the substrate-containing form, "transforming" with the idenity matrix (there's probably an easier way to do this). 5) Using mapman, I subtracted the apo map from the substrate-containing map. The resulting map was good for seeing conformational changes that apparently coincide with substrate soaking however it doesn't look like my substrate (or reaction product) is bound in this case : ( I suspected this would be the case. Off to my other data sets! Thanks again for all you help! Andrew Robinson CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 29 April 2007 |
| ProteinCrystallography.org: Copyright 2006-2008 by Quid United Ltd |