[sharp-discuss] Error during heavy atom finding

[abhimanyu singh]

Thanks Mark and Clemens for your suggestions. By both the ways i.e. by
cutting the data to lower resolution as well as by providing a list of
heavy atom sites in a separate file worked fine.



Regards,
Abhi

On Tue, Oct 30, 2012 at 7:54 PM, Clemens Vonrhein <
vonrhein at globalphasing.com> wrote:

> Dear Abhimanyu,
>
> On Tue, Oct 30, 2012 at 05:06:28PM +0100, abhimanyu singh wrote:
> > Recently I have collected a Se-SAD data set diffracting at around 1.7A in
> > I23 space group and am trying to process it through Autosharp.
>
> Sounds good.
>
> > While running when the program tries to find heavy atom sites using
> > ShelxD it terminates reporting "ARRAYS TOO SMALL TO STORE REFLECTION
> > DATA - TRY -L1" error.
>
> That seems to point to an error in SHELXD? Which version are you
>  running? The latest or the latest beta version of SHELXD?
>
> > Have any one ever encountered such an error and could suggest me any
> > possible reason behind it?
>
> You simply seem to have too many reflections (very large cell?). Two
> possibilities I could think of:
>
>   1. run autoSHARP with lower-resolution data (eg. cut at 2.5A): that
>      should be enough for finding your Se sites (if it is possible at
>      all).
>
>      If you run this autoSHARP job only to the heavy-atom detection
>      stage, you will get a set of initial sites (in a *.hatom file -
>      basically fractional coordinates). Put this *.hatom file into
>      your sharpfiles/datafiles directory.
>
>      Then re-run the same autoSHARP job again, but:
>
>        * use all data up to 1.7A
>
>        * pick the *.hatom file you just copied over.
>
>      Now autoSHRP will skip the HA detection with SHELXD (avoiding
>      that error) and start with the sites found in the previous 2.5A
>      run. But since you have all data now, it should give you phases,
>      maps and (hopefully) model to 1.7A.
>
>   2. you could write a shelxd wrapper to supply this -L1 flag (never
>      came across that before though) and point
>      $SHARP_home/machines/*/shelx.setup to the location with that
>      rapper (and a link to the true shelxc binary)?
>
> I would go for option 1: it also shows you how one can run autoSHARP
> with a starting set of known HA positions (which could come from all
> kind of external programs or calculations you did). This is very
> sueful if the default way of running SHELXC/D inside autoSHARP doesn't
> give you a good enough answer ... or stops with a warning message like
> you just hit upon.
>
> Kind regards
>
> Clemens Vonrhein
>
> --
>
> ***************************************************************
> * Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
> *
> *  Global Phasing Ltd.
> *  Sheraton House, Castle Park
> *  Cambridge CB3 0AX, UK
> *--------------------------------------------------------------
> * BUSTER Development Group      (http://www.globalphasing.com)
> ***************************************************************
>



-- 
*Abhimanyu Kumar Singh
*Ph.D. Student
Department of Macromolecular Structures
National Center for Biotechnology (CNB-CSIC)
C/ Darwin 3, Campus de Cantoblanco,
28049 Madrid, Spain.
E-Mail: abhimanyu.singh at cnb.csic.es
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