[buster-discuss] Error in assignment of symmetry operators

[Clemens Vonrhein]

Dear Radu,

Dale beat us to a suggested solution ;-)

Actually, BUSTER should check for the molecule being too far away from
the origin (more than 2 unit cells) and should fix this automatically
as part of the initial 'pdbchk' stage. But maybe this default step was
disabled or an odd combination of unit cell dimensions, molecule shape
or stray buffer molecules made this check fail.

What do you get when running

  pdbchk -p your.pdb -o test.pdb

Does it mention the "model rather far away from origin" issue?

Cheers

Clemens

On Tue, Jun 20, 2017 at 06:01:56PM +0100, A. Radu Aricescu wrote:
> Hi Dale,
> 
> The molecule was a couple of unit cells away, and indeed moving it closer to the origin solved the problem. The error message suggested this correctly, and I must have made a mistake when trying to do the move first time. But now it all works very well.
> 
> Best wishes,
> 
> Radu
> 
> 
> ---- Original message ----
> >Date: Tue, 20 Jun 2017 09:21:05 -0700
> >From: "buster-discuss" <buster-discuss-bounces at globalphasing.com> (on behalf of Dale Tronrud <detBB at daletronrud.com>)
> >Subject: Re: [buster-discuss] Error in assignment of symmetry operators  
> >To: buster-discuss at globalphasing.com
> >
> >
> >   Is the molecule unusually far from the origin?
> >
> >Dale Tronrud
> >
> >On 6/20/2017 5:44 AM, A. Radu Aricescu wrote:
> >> Dear All,
> >> 
> >> I am trying to refine a model in Buster, but hit the following problem:
> >> 
> >> ERROR : [run_buster-0046] unable to create initial SCREEN
> >>          output with gelly - see
> >>          refine/01-BUSTER/Cycle-1/gelly_screen.log)
> >> 
> >> Looking in the gelly_screen.log, the problem reported is:
> >> 
> >>       Getting symmetry operators from TNT. 
> >>           gelly will classify symmetry using pdb-like convention: 
> >>                SYMOP   SYMMETRY
> >>               NNNMMM   OPERATOR
> >>                 1555   X,Y,Z
> >>                 2555   -X,Y,-Z
> >>                 3555   1/2+X,1/2+Y,Z
> >>                 4555   1/2-X,1/2+Y,-Z
> >>           where NNN -> operator number and MMM -> translation vector
> >>  
> >> *** ERROR in assignment of symmetry operators NNNMMM (M<1 or M>9).
> >> *** ERROR maybe the molecules are far away from the origin.
> >> 
> >> I tried everything I could think of to fix this, no luck so far.... Would be very grateful for any advice!
> >> 
> >> Best wishes,
> >> 
> >> Radu
> >> PS: space group is C2
> >> 
> >> ------------------------------------------
> >> A. Radu Aricescu, PhD
> >> 
> >> University of Oxford
> >> Wellcome Trust Centre for Human Genetics
> >> Division of Structural Biology
> >> Roosevelt Drive, Oxford OX3 7BN
> >> United Kingdom
> >> Phone: +44-1865-287564
> >> Fax: +44-1865-287547
> >> https://www.strubi.ox.ac.uk/research/a-radu-aricescu
> >> _______________________________________________
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> >> buster-discuss at globalphasing.com
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> >> 
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* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
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