Dear Nicholas,
Why do you want to do the same rebuilding twice? Once in the P212121 map
and once guided by the rotated P212121 map?
What I usually do in these cases, and which seems more efficient to me,
is to first complete rebuilding and refinement of the better defined
p212121 structure and then superimpose the refined coordinates onto your
P213 molecule. Since you probably have 3 molecules in the asymmetric
unit in P212121 and 1 molecule in P213, you could superimpose the 3
p212121 molecules onto your single P213 molecule.
Then either you rebuild your P213 molecule, guided by the coordinates of
the P212121 structures, or you rebuild one of the P212121 molecules into
the p213 structure, just like one does with molecular replacement.
My 2 cents,
Herman
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Nicholas Keep
Sent: Thursday, January 17, 2013 3:09 PM
To: [log in to unmask]
Subject: [ccp4bb] P212121 and P213
I have a structure which normally crystallises in P213 but one data set
the edges became slightly non-equivalent in length by a couple of
angstroms and the data process in P212121
P212121 symmetry operators appears to be a subset of P213
http://img.chem.ucl.ac.uk/sgp/large/019az1.htm
http://img.chem.ucl.ac.uk/sgp/large/198az1.htm
(Not absolutely sure the above are world viewable)
Naively I expected the two structures to roughly align. However they
don't there appears to be some change of axes between them.
The transform of the P213 onto the P212121 structure is
0.03345 -0.9977 -0.0598
-0.9994 0.03402 -0.08653
0.01066 0.05929 -0.9982
-18.16 -57.18 21.39
This is clearly close to
0 -1 0
-1 0 0
0 0 -1
-0.25 -.75 0.25 in fractionals.
Applying either the exact transformation or the regularised one with
ether indexing of p213 ie original and k h -l
http://www.ccp4.ac.uk/html/reindexing.html
the rfactors are well above 50% and don't drop.
Any suggestions of what I am doing wrong or is this not going to work
(tried MR into the reindexed data and that does not align either- in
fact I have tried quite a lot things)
The reason for trying to get the two structures on the same axes is to
compare the electron densities. The P212121 seems to have some of the
disorder loops better defined.
Using the Coot transform map by LSQ superpose is quite good BUT it would
be better if it were another map other than the refinement map that is
transformed as I then want to refine the unmoved structure into the
unmoved map guided by the moved map and that involved a lot of changes
of map selection.
Thanks
nick
--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences Birkbeck, University of London, Malet
Street, Bloomsbury LONDON WC1E 7HX
email [log in to unmask]
Telephone 020-7631-6852 (Room G54a Office)
020-7631-6800 (Department Office)
Fax 020-7631-6803
If you want to access me in person you have to come to the
crystallography entrance and ring me or the department office from the
internal phone by the door
--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences Birkbeck, University of London, Malet
Street, Bloomsbury LONDON WC1E 7HX
email [log in to unmask]
Telephone 020-7631-6852 (Room G54a Office)
020-7631-6800 (Department Office)
Fax 020-7631-6803
If you want to access me in person you have to come to the
crystallography entrance and ring me or the department office from the
internal phone by the door
