[sharp-discuss] autosharp with unmerged scalepack file

[Clemens Vonrhein]

Dear Jinsong,

don't be mislead by the scalepack 'unmerged' data. It is not what we
mean when talking aout unmerged data ourselfs. For the treatement of
radiation damage data in SHARP we need unmerged data that has all the
dose-dependent information available. The scalepack data doesn't
qualify for that (at the moment we use SCALA unmerged output for that
in SHARP).

Have a look at the paper by M. Schiltz on that.

Cheers

Clemens

On Thu, Jan 19, 2006 at 02:07:03PM +0800, Jinsong Liu wrote:
> Thanks  Jan,
> 
> Switching from standard mode to expert put the space group option back and
> the problem was solved. The ccp4i problem may be a bug.
> 
> To use unmerged data was inspired by a talk Gerard gave. My data has severe
> radiation damage, and he said using unmerged data and some time-dependent
> compensation model, the anomalous signal will be enhanced somehow. Anyone
> has some more real life example on this issue?
> 
> Jinsong
> 
> 
> On 1/19/06, Jan Abendroth <JanAbend at u.washington.edu> wrote:
> >
> > Jinsong,
> > as far as I remember, switching from standard to expert mode helped with
> > the space group issues and non-merged data. However, I did not see any
> > difference between using unmerged and merged data after all.
> >
> > Two more things that I noticed with the new Sharp version:
> >
> >     *  the output mtz-files always have HKLs to 1.5AA resolution,
> >       although the input data barely make it to 3AA...
> >     * Autosharp does not seem to stick to the resolution limits defined
> >       by the user in the input file. Instead, it uses the highest
> >       resolution as in the input mtz-file. In non-auto-Sharp, however,
> >
> > Are these general observations or are there problems with our
> > installation?
> >
> > Cheers
> > Jan
> >
> > Jinsong Liu wrote:
> >
> > > Dear All,
> > >
> > > Anyone has the Autosharp running with unmerged scalepack file? I took
> > > a scalepack file (with "no merge original index" option) and run
> > > autosharp. There is only "unit cell" in the autosharp setup, so I put
> > > in the cell constant, and the sca file has the space group info in the
> > > header. But the autosharp run failed and complained "difference in
> > > space group, input=(empty) from file=C2221". I can see nowhere I can
> > > manually input the space group information.
> > >
> > > So I tried the ccp4i approach and hope I could get around with this
> > > problem. But the run also failed, but with difference error message,
> > > "ERROR : data file output.sca for wavelength 1 is not a MTZ file". In
> > > the ccp4i window I DID choose the "input file is in SCALEPACK
> > > (unmerged) format" option.
> > >
> > > I'm very confused now. Anyone can give me a clue what went wrong?
> > >
> > > Many thanks.
> > >
> > > Jinsong
> > >
> > >Jinsong Liu, Ph.D.
> > >Investigator
> > >Guangzhou Institute of Biomedicine and Health (GIBH)
> > >Chinese Academy of Sciences
> > >
> > >Guangzhou ( Canton ) 510663, China
> > >Phone: 86-20-32290431 (Office)
> > >E-mail: liu_jinsong at gibh.org
> > >Second E-mail:
> > >jinsong.liu at gmail.com
> > >
> > >
> > >
> > >
> > >
> > >------------------------------------------------------------------------
> > >
> > >_______________________________________________
> > >sharp-discuss mailing list
> > >sharp-discuss at globalphasing.com
> > >http://www.globalphasing.com/mailman/listinfo/sharp-discuss
> > >
> > >
> >
> >
> > --
> > Jan Abendroth
> > Howard Hughes Medical Institute and
> > University of Washington
> > 1959 NE Pacific Street, K-426
> > Box 357742
> > Seattle, WA-98195
> > phone: +1-206-616-4510
> > fax:   +1-206-685-7002
> >
> >
> >

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