[buster-discuss] Refining incomplete structure

[Clemens Vonrhein]

Dear Anna,

On Tue, Dec 03, 2013 at 02:24:29PM +0100, Anna Suarez Larsson wrote:
> I am trying to refine an incomplete structure. We have not been able
> to localised 100 of 360 residues due to high flexibility. Resolution
> is 3 Å and when using refmac the R values are slowly increasing
> during refinement.

Is there anything else that could cause this? If you have NCS you
should use the "-autoncs" flag in BUSTER. See

  http://www.globalphasing.com/buster/manual/gelly/manual/gelly4A.html

and

  http://www.globalphasing.com/buster/wiki/plugin/attachments/DocumentationTopPage/buster_reference_card.pdf

> Are there any way in Buster to make the program know there are more
> atoms present in the asymmetric unit than in the model?

Yes, the "MissingAtoms" macro - see

  refine -M list

So you could try running BUSTER with (100 residues ~ 1100 atoms)

  refine -p your.pdb -m your.mtz \
         -autoncs -M MissingAtoms nmiss=1100 \
         ... -d out.01 | tee out.01.lis

and see what it does. Make sure to check the reciprocal-space
correlation plot with

  graph_autobuster_recipCC -d out.01

See

  http://www.globalphasing.com/buster/wiki/index.cgi?BusterCCplot
  http://www.globalphasing.com/buster/wiki/index.cgi?BRrecipCCplot

Kind regards

Clemens & Claus (for buster-develop)

-- 

***************************************************************
* 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)
***************************************************************