[phenixbb] phenix-cns conversion

Sean Johnson sean.johnson at usu.edu
Tue Apr 8 15:12:45 PDT 2008

What is the best way to convert phases obtained from phenix to a usable 
cns format?  I have 3.6 A maps that were SAD phased and density modified 
using phenix.  I now want to use some of the cns refinement options - 
like torsion angle refinement.  I tried converting structure factors and 
HL coefficients to cns format using phenix.reflection_file_converter, 
but when I run cns input files, I start getting errors like the ones 
shown below (this is from density_modify.inp):

 Program version= 1.2 File version= 1.2
 %XMAPASU-AUTOmem: increasing memory allocation to    2000000
 Minimum brick that covers asymmetric unit:
   A=     0,...,   150  B=     0,...,   150  C=     0,...,    36
 Sum of     21042 elements =             21042.0000
 SHOW: average of    810150 elements=                 0.0000
 ANOMalous=FALSe {OFF}
 XMPST: average =   0.0000  minimum =   0.0000  maximum =   0.0000
 XMPST: r.m.s.  =   0.0000     norm =   0.0000
 XMHISTO: (default from map) RHOMIN and RHOMAX =   0.0000   0.0000
 %XMHISTO-ERR:  a complete flat map.
 XMHISTO: (default from map) SLOT width =  0.000000
 %XMHISTO-ERR: the SLOT width is too small   0.00000
 XMHISTO: the number of slots MBINS=10000 and width SLOT=   0.0000
 %XDOTYPE-ERR: Variable/type mismatch:
      do (masksol=1) (real(automap) <= $cutoff)
 %DO-ERR: Data type mismatch.  Selection must be a logical expression.:
      do (masksol=1) (real(automap) <= $cutoff)
 %SHOW error encountered: There were errors in DO expression.
   (CNS is in mode: SET ABORT=NORMal END)
 ABORT mode will terminate program execution.
 Program will stop immediately.

I'm guessing that the problem has to do with the way I am converting the 
data to cns (since I have beautiful maps from phenix), but I'm really 
stuck right now.  Any guidance would be appreciated.

Sean Johnson

Sean Johnson, PhD
R. Gaurth Hansen Assistant Professor
Utah State University
Department of Chemistry and Biochemistry
0300 Old Main Hill
Logan, UT 84322-0300
(435) 797-2089
(435) 797-3390 (fax)
sean.johnson at usu.edu

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