 |
 |
Hi
I would like to convert a map into SFs to use for molecular replacement. Read on if you think you can help.
I have a 3.7A MAD data set and a few 30% similar homology models for crystal in i222 space group. The combination of the two pieces of information generated solvent flattened phases which reflect unique information and have a FOM of 0.65. Workable, but certainly any model I build is inherently poor.
I have new data for the same protein (2 mols in the ASU now) in C2 space group with data to 2.1A. The poor models (original models and an attempt at a "better" built model from the 3.7A phases) do not work as molecular replacement solutions in Phaser or MolRep. It would be better if I could use the i222-3.7A map for the molecular replacement into the new space group.
PHASER manual says "This density has been cut out and converted to structure factors in a large cell"
So, how do I do that?
I have Fcalc/PHIcalc from RESOLVE in the i222 cell. I can use the sftools facility to expand the data to a P1 cell. This actually works as a MR model for PHASER and the rotation function is much higher than seen with any PDB model, AND there are actually two high Z-score hits which is exactly what I expect/want. The program continues into the fast translation function and fails with:
------------
ENSEMBLE map
------------
Fixed MR solutions
(No solutions of this type)
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
The program run with command: phaser
has failed with error message
child killed: segmentation violation
I figure my problem is with the Extent and Center data that is given to PHASER. I don't know what the EXTENT is for a mtz file - only for a map. But I'm giving it a MTZ. In my run above I gave it an extent from the original i222 resolve.mbk I made, but I can't imagine this is useful.
I can give a CENTRE of the model that I've built in the i222 map but does this have any relation to my new P1 cell? Sort of...
I also think that now my P1 cell/mtz file has eight molecules in it and my guess is that PHASER wants one molecule in a P1 cell. So how would I do that? I tried using the map to make SFs but which cell do I use? Do I generate a random/empty P1 cell mtz file and the use the Clipper "map SF from map" utility? How to generate a blank MTZ file? I can generate Fcalc/PhiCalc in I222 and C2 space groups easily, but again how to get them into the P1 space group and after all that - what extend would I use then?
Any help would be appreciated.
Heidi
University of Utah
Biochemistry