Re: [ccp4bb] XDS to MTZ for SOLVE

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CCP4bb <-- 2007 <-- March 2007 <-- 07 March 2007

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Subject: XDS to MTZ for SOLVE
From: "Santarsiero, Bernard D {- dot -} " bds {- at -} UIC {- dot -} EDU
Date: 2007-03-07

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Subject: Re: XDS to MTZ for SOLVE
From: "Winter, G (Graeme)" g {- dot -} winter {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-03-07

Hi,

I believe that SOLVE can read MTZ format files directly so there is no
need to convert it to anything else. However if you do feel the need to
perform some file conversion I would get mtz2sca (google it) and convert
the MTZ intensities to scalepack format, then read these in as
PREMERGED. That has always appeared to do "sensible things".

Somewhere out there there is also a program called xds2sca which will
read in the unmerged output of XSCALE (MERGE=FALSE FRIEDEL'S_LAW=FALSE)
and produce an unmerged scalepack file that SOLVE will read in as
UNMERGED.

In either case you will need READ_INTENSTIES as that is what you are
doing. There are example scripts at

http://www.solve.lanl.gov

Which show how to format the input for each of these examples.

Hope this helps.

Cheers,

Graeme

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Santarsiero, Bernard D.
Sent: 07 March 2007 15:19
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] XDS to MTZ for SOLVE

Not purely a ccp4 question, but an MTZ file is involved, so stick with
me.

I've collected a SAD data set, and processed with XDS. I can use XDSCONV
to generate an MTZ, SHELX, and CNS file. I chose the MTZ file since it
keeps the intensities. SHELX does too (the F**2), but has separate lines
for (h,k,l) and (-h,-k,-l). The MTZ file has hkl,IMEAN, SIGIMEAN, I+,
SIGI+, I-, SIGI-.

I used mtzdump (or could use MTZVARIOUS) to convert this file to a
simple ASCII file, and then extracted just the hkl, I+, SIGI+, I-,
SIGI-. Since
CCP4 fills in all of the reflections in an ASU, I removed those
reflection entries with SIGIMEAN = -999.0.

I have a file with has some entries with -999 (for the non-measured
value), especially those in the centric zones.

For SOLVE, does it identify entries with a value of -999 as a
placeholder, or should I entirely removed those from the data file? I
used the options

PREMERGED
READFORMATTED
READ_INTENSITIES

in SOLVE. What if I measured I- but I+? That's why I left them all in.

Suggestions on what is best for the solve run? I'm concerned that it's
interpretting the -999 as a real measurement.

Bernie Santarsiero

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CCP4bb <-- 2007 <-- March 2007 <-- 07 March 2007

Previous message:
Subject: XDS to MTZ for SOLVE
From: "Santarsiero, Bernard D {- dot -} " bds {- at -} UIC {- dot -} EDU
Date: 2007-03-07

Next message:
Subject: Re: How to get rid of Membrane formed on hanging droplets?
From: Edwin Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU
Date: 2007-03-07