Trying to calculate a difference map from a dataset downloaded from the RCSB
and one I have. The following applies:
Object find the difference between two bound ligands of the same structure
in the same space group.
My following work path has been:
1) Convert mmCIF to mtz (RCSB data set)
2)
I just looked at a previous thread by Dale Tronrud that explains this.
here it is:
Re: [ccp4bb] Fo-Fo Difference Map
Dale Tronrud
Mon, 03 May 2010 16:19:46 -0700
I've struggled with getting CCP4 to calculate Fo-Fo maps, since I
usually use other software. The tricks are that the data sets
Replacing the Coot step by FFT works too.
An additional benefit of the Coot approach is that you can use
LSQ-matched maps and maps on different grids and space groups. (I was
under the impression that that was not quite so easy with FFT.)
Also worth noting, Coot does not (yet) do
Yes - you are.
-
There are some extra steps.
Download pdbs and mtz files
csymmmatch -pdbin-ref 1.pdb -pdbin 2.pdb -origin-hand -pdbout 2-to-1.pdb
That checks they are on same origin and symmetry equivalent.
refmac for 1.pdb
refmac for 2-to-1.pdb
cad to merge two refmac outputs.
You will
2) Scale F-holo and F-apo. Use Experimental Phasing, Data
Preparation, Scale and Analyse Data Sets, Scale refinement using
Scaleit. Don't include anomalous differences unless your interest is in
changing anomalous scatterers. My notes indicate that Fhscal works
better but does
