questions regarding program MLPHARE

matte at sask.usask.ca matte at sask.usask.ca
Sat Jan 23 23:56:20 EST 1993


I have been doing MIR calculations using the program MLPHARE from the CCP4 
program suite (V 2.1.3), and would appreciate answers to any of the following 
questions:

During these calculations, I do refinement and calculate phases on all cycles 
(say 10). I notice that some statistics relevant to the refinement are output 
at the end of cycle 9, (what the program calls the last refinement cycle), and 
again for the last phasing cycle (cycle 10).  My (simplistic) understanding of 
phase refinement is that the heavy-atom parameters are adjusted while minimiz-
ing the difference betwen FPH(obs) and FPH(calc), and then phases are 
calculated based on these new parameters.  If this is so, why are statistics 
given for the final refinement and phasing cycles seperately, and which of 
these are the ones that should be quoted for purposes of publication, etc  ? I 
have noticed that the statistics (ie. the Cullis R-factor and phasing power) 
from the last refinement cycle (given as cycle #9) are always quite a bit 
better than on the last phasing cycle (#10). The other thing is that the 
occupancy and/or temperature factor shifts for a given heavy-atom are quite a 
bit larger on the final phasing cycle than on the final refinement cycle. 
Looking at all of the previous cycles (except #10) it would seem that 
everything has converged properly. My final question is as to why it is not 
possible to output "most probable" phase values to the mtz reflection file, 
although there is a PHIPR LABOUT card in the program ?  The message I get back 
when I ask for PHIPR is that it is an invalid program label, or something 
related to that.  

Any information will be very much appreciated !

						Thanks,

						Allan Matte
`						Department of Biochemistry
						University of Saskatchewan
						matte at sask.usask.ca		
						




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