Hi,
The refinement program generates an mtz file with map coefficients
(including difference Fourier coefficients) so you should use that one
for model rebuilding in coot;
for the next refinement rounds, at the beginning of each round you
should provide the initial mtz file coming from data processing and post
processing (1 in your terminology I suppose). This is because several
refinement programs scale the Fobs (and sigmaFobs). Refmac is one of
them I think;
for data deposition, you deposit the same mtz file (1), and if you also
wish to deposit map coefficients you can also extract the map
coefficients from the "final" refinement and map calculation round mtz
(using, say, sftools) and deposit those.
Phaser does not carry out model refinement per se (adjusting atom
positions and temperature factors). But the map coefficients present in
the mtz file are generated in the same way (Sigmaa coefficients) with
Phaser and with Refmac. There might be small difference in terms of the
program code used internally but that shouldn't make much of a difference.
Since a model that has "seen" refmac is (normally) improved, the
electron density maps generated using the refmac mtz should be improved
wrt the maps coming directly from Phaser (molecular replacement).
Normally, the model you refine will have had the differences in the
sequence between molecular replacement search model and 'your' structure
corrected (gradually?), the solvent model is introduced and improved,
ligands, ions etc are being introduced... Thus the maps improve seen
that your model should reflect more and more what is present in the
crystal as you build and refine.
HTH,
Fred.
Uma Ratu wrote:
Hello,
I have a question about .mtz files used in model building.
Here is how I did:
Diffraction data - HKL 2000: .sca
CCp4i: scalepack2mtz: .mtz (1)
Phaser: In: template pdb & .mtz(1)
Out: model .pdb(1) & .mtz(2)
Refmac5: model .pdb(2) & .mtz(3)
Here is the question:
1. Coot check and refinment: which mtz file shoudl I use?
2. With further refinemnt by refmac5, which mtz file should I use?
3. When I deposit data, which mtz file to use?
4. What is the difference between .mtz(1) and the .mtz files generated
from "phaser" and "refmac"?
Thank you for advice
Ros
