Hi Aleks:
Maybe you can try CNS ( Initial refinement by simulated annealing) also. It may
help to get rid of the model bias and takes short time to run.
Xiaodi
> Date: Wed, 29 Apr 2015 13:52:53 +0200
> From: frederic.velli...@ibs.fr
> Subject: Re: [ccp4bb] model bias
> To: CCP4BB@JISCMAIL.AC.UK
>
> Hello,
>
> I would certainly try the "usual approaches" (map coefficients that are
> less sensitive to model-bias, i.e. Sigmaa; OMIT maps - there are several
> of these which can be calculated). In addition, you may have a look at
> the approach of Liu and Xiong (2014, J. Mol. Biol. 426, 980-993). It is
> a well known technique (applying a negative temperature factor to
> amplitudes, for map sharpening) but this paper describes a systematic
> study indicating improvement whatever the situation.
>
> As usual in macromolecular crystallography, confidence is gained by the
> use of several approaches.
>
> HTH,
>
> Fred.
>
> On 29/04/15 13:16, Aleksandar Bijelic wrote:
> > Dear CCP4 users,
> >
> > I am currently solving a structure (2.8-2.9 A resolution) of a protein
> > complexed with a ligand using MR with the apo-form of this protein as
> > model (resolution of the model is 2.4). After MR-phasing I performed a
> > regular autobuild run giving me good outputs and thus I refined the
> > best pdb leading to good values according to R-values and geometry,
> > however, the denstiy doesn´t look well (but I think it´s due to the
> > moderate resolution). Now I want to get sure if the side chains which
> > are involved in the ligand binding are correctly positioned. However,
> > the active site is suspicously similar to the active site of the model
> > (apo-form) and so I am afraid that this could be due to model bias.
> > My question is how to check and to get rid of the bias (if present) at
> > this stage (after several refinements). I read the publication of
> > Terwilliger about iterative-build OMIT maps but since I am a bloody
> > novice in this field I didn´t really understand it. I originally
> > thought iterative-build OMIT maps are performed to compare the output
> > map with one´s map in order to detect uncertainties, but what to do
> > next? Or should I start from the beginning but how to proceed than,
> > what should I do (I am using Phenix via GUI) ... Is it possible and
> > reasonable to run autobuild with iterative omit map option? Or is it
> > only reasonable if experimental phases are available? I didn´t run
> > iterative-build OMIT maps yet because I am not sure how to run it
> > correctly (what method is the best?) and at my institute the run will
> > take more than 1 day and I don´t want to block one computer until I am
> > not sure if it is reasonable. I hope you can give me some advice and
> > help me. Thank you in advance.
> >
> > Regards,
> >
> > Aleks
> >
>
>
> --
> Fred. Vellieux (B.Sc., Ph.D., hdr)
>
> IBS / ELMA
> Campus EPN
> 71 avenue des Martyrs
> CS 10090
> F-38044 Grenoble Cedex 9
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