[buster-discuss] Error in assignment of symmetry operators

[A. Radu Aricescu]

Dear Clemens,

Yes, it writes:

 WARNING : model rather far away from origin! A shift of
           (0,1,-2) will bring it closer to the origin.
 
And then:

 NOTE : applied above shift to model

However, this step didn't happen.... Checking my script, this line explains why:

UsePdbchk=no -d refine

I knew it must be my fault :-)

Best wishes,

Radu


---- Original message ----
>Date: Tue, 20 Jun 2017 21:30:12 +0100
>From: Clemens Vonrhein <vonrhein at globalphasing.com>  
>Subject: Re: [buster-discuss] Error in assignment of symmetry operators  
>To: "A. Radu Aricescu" <radu at strubi.ox.ac.uk>
>Cc: Dale Tronrud <detBB at daletronrud.com>,buster-discuss at globalphasing.com
>
>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
>> >> _______________________________________________
>> >> buster-discuss mailing list
>> >> buster-discuss at globalphasing.com
>> >> https://www.globalphasing.com/mailman/listinfo/buster-discuss
>> >> 
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>-- 
>
>*--------------------------------------------------------------
>* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
>* Global Phasing Ltd., Sheraton House, Castle Park 
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