Dear all,
Thank you for your replies,
I actually saw the options in coot that Chris and others suggested and
I already tried it before, but for some reason it did not work for me.
Maybe I`m doing something wrong. So I open in coot pdb1 and map1 for
mutant 1 and pbd2 and map2 for mutant 2. Then I go to extension map,
transform by LSQ model fit, I specify the reference (pdb1) and moving
(pdb2) structures, specify the residue and the radius (by the way
there is no option to specify the map). I assume coot does it
automatically, since I specify the moving and reference structures.
Then, all coot is doing, is creating transformed copy of pdb2 (which
is in alignment with pdb1), and a transformed map. But this
transformed map does not match the transformed copy of pdb2. Actually
it does not match any of the pdbs?
Thank you, Milya.
Quoting [email protected]:
Dear Milya,
Last year, we were facing the exact problem you mentioned.
I contacted Paul Emsley (author of COOT) who programmed a little routine
wich is part of the general release of the program:
In COOT version 0.5.2, go to
Extensions > Maps ... > Transform map by LSQ model fit ...
You will need to specify two structures (Reference and Moving), as well
as the map to be transformed.
That should do the trick.
Thanks,
Chris
-----Original Message-----
From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of
Milya Davlieva
Sent: Mon, September 07,2009 6:28
To: [email protected]
Subject: [ccp4bb] Alignment of Electron Density Map for structures that
have different space groups
Dear all,
I need to make a figure which needs to consist of 2 aligned pdb files
and their electron density maps for the structures of two mutants (with
different space groups). I'm able to do this when there are two
structures that have the same space group. Could, you, please, help me
to find a way to do this for structures with different space groups?
Thank you very much for your help,
Dr. Milya Davlieva
Rice University
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