Re: [ccp4bb] .phs file conversion

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: .phs file conversion
From: Bart Hazes Bart {- dot -} Hazes {- at -} UALBERTA {- dot -} CA
Date: 2009-03-04

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Subject: Re: .phs file conversion
From: tommi kajander tommi {- dot -} kajander {- at -} HELSINKI {- dot -} FI
Date: 2009-03-05

Subject: Re: .phs file conversion
From: "Mark A {- dot -} White" white {- at -} XRAY {- dot -} UTMB {- dot -} EDU
Date: 2009-03-04

From: Mark A. White
To: John Bruning
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] .phs file conversion
Date: Wed, 4 Mar 2009 14:16:47 -0600

John,

The PHS file has the coefficients to make a map, along with the cell
parameters, but is not itself a map. There are a few choices.

1) View the PHS file in XtalView (xfit) or MIFit, which is where it was
meant to be viewed. COOT will also display maps from PHS files. The
PDB file must have the correct CRYST1 entry. Xfit has an output option
to save the map coefficients as an MTZ file. This requires a working
CCP4 installation.

2) Use CCP4 to convert the PHS file into an MTZ and then to a CCP4 MAP,
using FFT. This can then be viewed in PYMOL.

##############################################################################
# Convert LSCALE.PHS file to MTZ
##############################################################################
f2mtz HKLIN pmb_lscale.phs HKLOUT pmb_lscale.mtz << f2mtz_eof >
f2mtz.html
TITLE MTZ from PHSS From FoFc_calc.inp -> pmb_cns2phs.pl
PNAME D999
DNAME D999
CELL 86.15 72.65 25.89 90.00 90.00 90.00
LABOUT H K L FO FC PHIC
CTYPout H H H F F P
FORMAT '(2X,3F5.0,3F10.3)'
SYMM 18
f2mtz_eof
#

Note that the format of the PHS file is not standardized, but that F2MTZ
requires a well defined fixed format.

Good luck,

Mark

On Wed, 2009-03-04 at 13:48 -0600, John Bruning wrote:

> Hi,
>
> I have a .phs file with map coefficients that I would like to open in
> pymol. So, I would like to convert the file to either a ccp4 or cns
> map file, or a file format that pymol will recognize. I do not have
> an .mtz file with the same map coefficients included. Can anyone help
> me?
>
>
> Thanks,
> John

Yours sincerely,

Mark A. White, Ph.D.
Assistant Professor, Dept. Biochemistry and Molecular Biology,
Manager, Sealy Center for Structural Biology and Molecular Biophysics
X-ray Crystallography Laboratory,
Basic Science Building, Room 6.660 C
University of Texas Medical Branch
Galveston, TX 77555-0647
Tel. (409) 747-4747
Cell. (409) 539-9138
Fax. (409) 747-4745
mailto://white@xray.utmb.edu
http://xray.utmb.edu
http://xray.utmb.edu/~white

Yours sincerely,

Mark A. White, Ph.D.
Assistant Professor, Dept. Biochemistry and Molecular Biology,
Manager, Sealy Center for Structural Biology and Molecular Biophysics
X-ray Crystallography Laboratory,
Basic Science Building, Room 6.660 C
University of Texas Medical Branch
Galveston, TX 77555-0647
Tel. (409) 747-4747
Cell. (409) 539-9138
Fax. (409) 747-4745
mailto://white@xray.utmb.edu
http://xray.utmb.edu
http://xray.utmb.edu/~white

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: .phs file conversion
From: Bart Hazes Bart {- dot -} Hazes {- at -} UALBERTA {- dot -} CA
Date: 2009-03-04

Next message:
Subject: Re: .phs file conversion
From: tommi kajander tommi {- dot -} kajander {- at -} HELSINKI {- dot -} FI
Date: 2009-03-05