Re: [ccp4bb]: conversion of .phs phase file (xtalview) to .mtz format

[Paul Hubbard <phubbard@post.its.mcw.edu>]

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STOP!!!! I never said that! The "unkown column" in your file is unlikely to be
packed H-L coefficients. The script I sent was taken from a PHASIT file as an
example, where H-L coeffs. are packed in 2 columns. If more of these "unknown"
values are 1.0 - my guess is that they are FreeRFlags for X-validation.

How to make an O map from an MTZ file:

1) Click on the 'Map & Mask Utilities" module

2) Click on "Run FFT - Create Map"

3)"Run FFT" to generate "simple" map
Output map in "O" format to cover "asymmetic unit"

F1 = FP Sigma = Unassigned (though you should copy this from an original file and
use it - SIGFP)
PHI = PHIS Weight = FOM

NOTE: If you have a PDB file, you can generate a map surrounding the atoms by
selecting "all atoms in a PDB file" instead of "asymmetric unit". Then supply the
PDB file.



Ram Thaimattam wrote:

> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> Dear All,
> thanks for so many suggestions. i am able to pick you up though quite slowly
> as i am a beginner. I tried the options suggested to me by Eleanor and
> Ramagopal and things seems to working fine in a sense that the assigned
> jobs to CCP4 is successfully completed. I am using CCP4 interface for
> performing fft and cad.
> and following script is used to get .mtz file from .phs output from shelxe.
> /programs/ccp4/bin/f2mtz HKLIN anzn.phs HKLOUT tmp3.mtz << e
> SYMM P21212
> CELL 47.294 58.715 19.324 90.000 90.000 90.000
> format '(3f4.0,f11.2,f8.2,f8.1,f8.2)'
> skipline 0
> LABOUT H K L FP FOM PHIS X
> CTYPOUT H H H F W P R
> END
> e
>
> the maps generated by using cad or fft from the above mtz file could not be
> seen in O. and O reports that the Volume for contouring not in map volume"
> when when clicked on the Rad contour. I am not sure if i should go through the
> option of CAD to generate map as all the information is contained in the .phs
> shelxe output.
> let me clarify the format of .phs file from shelxe which has been already
> pointed by some.
> it contains columns related to h,k,l,Fo,fom,phi and a number in the seventh
> column (the HL coeffs. that is to be unpacked as suggested by AGS). otherwise
> the format of this .phs file should be h,k,l,Fo,fom,phi,HLA,HLB,HLC,HLD.
> This is where i stand now and learnt many things for being here and i would
> welcome any further suggestions.
> thanking you,
> ram

--
Paul Hubbard
Dept. of Biochemistry
Medical College of Wisconsin
Phone: 414-456 4305
Fax: 414-456 6510
URL: iris9.biochem.mcw.edu