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

["Frank Vondelft" <Frank.Vondelft@syrrx.com>]

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Hi Ram:

As far as I know, the last column in the shelxe output contains the
phase error.  

As far as the map contouring volume is concerned, O requires the loaded
map to be calculated over the volume of interest, i.e. if you're
considering the heavy atoms, you should extend (using mapmask) the map
to cover those atoms.  (The easy way to find the required limits is to
use the minimum and maximum x,y,z values of all the heavy atoms.)

An easier way, which bypasses all of mtzutils, fft, and mapmask, is to
use xtalview, which reads the .phs file directly and calculates the map
on the fly over the volume where you're centred. 

Good luck.
Phraenquex




> -----Original Message-----
> From: Ram Thaimattam [mailto:ram@alanine.ibch.poznan.pl]
> Sent: Thursday, April 04, 2002 3:45 AM
> To: ccp4bb@dl.ac.uk
> Subject: Re: [ccp4bb]: conversion of .phs phase file 
> (xtalview) to .mtz
> format
> 
> 
> ***  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
>


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