Re: [ccp4bb] Molecular replacement using a partial molecular replacement solution

[Herman . Schreuder]

Hi Mo,
Phaser sometimes rejects solutions because of clashes in the crystal
packing, which may be due to differences between the search model and
the target molecule. I would certainly recommend to play around with the
PACK keyword to see whether Phaser will find solutions if more clashes
are allowed.
 
Best regards,
Herman


________________________________

        From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
Behalf Of Mo Wong
        Sent: Monday, January 19, 2009 5:37 PM
        To: CCP4BB@JISCMAIL.AC.UK
        Subject: [ccp4bb] Molecular replacement using a partial
molecular replacement solution
        
        
        Hello,
        
        My problem: I have poorly phased 3.5A data which suggests 6
molecules per ASU, and using MolRep with the experimental phases
("search for model in the map") I have good solutions 3 of them. There
is a lot of empty electron density which needs to be filled with more
copies of the molecule. I have looked for NCS operators as I know this
will improve the map and help with model fitting (the Self Rot function
suggests I have at least 2-fold symmetry), but no luck yet. My current
focus is on using the 3-molecule partial solution as a starting point,
but since I'm not getting anywhere fast, I though I'd post to the
bulletin board.
        
        Can someone please either point me to a MolRep script that
allows me to fix the known solutions, use the experimental phases, and
search for (3?) more copies of the model, or tell if there is something
wrong with the following Phaser scripts below (....is it necessary to
apply an operator to the MolRep solution before reading into Phaser?).
        
        Thanks!
        
        #####
        phaser << eof
        
        MODE MR_FRF
        
        HKLIN overall_best_denmod_map_coeffs.mtz
        LABIN F = FP SIGF = SIGFP
        
        ENSEMBLE trimer PDBFILE trimer.pdb IDENTITY 0.25
        ENSEMBLE monomer PDBFILE monomer.pdb IDENTITY 0.25
        COMPOSITION PROTEIN SEQUENCE trimer.seq NUM 1
        COMPOSITION PROTEIN SEQUENCE monomer.seq NUM 3
        
        SOLU 6DIM ENSE trimer EULER 0 0 0 FRAC 0 0 0
        
        SEARCH ENSEMBLE monomer NUM 1
        
        ROOT AUTO_monomer
        
        eof
        #####
        phaser << eof
        
        MODE MR_FTF
        
        HKLIN overall_best_denmod_map_coeffs.mtz
        LABIN F = FP SIGF = SIGFP
        
        ENSEMBLE trimer PDBFILE trimer.pdb IDENTITY 0.25
        ENSEMBLE monomer PDBFILE monomer.pdb IDENTITY 0.25
        COMPOSITION PROTEIN SEQUENCE trimer.seq NUM 1
        COMPOSITION PROTEIN SEQUENCE monomer.seq NUM 3
        
        @AUTO_monomer.rlist
        
        ROOT AUTO_monomer2
        
        eof
        #####