Re: [ccp4bb]: Comments on ligands

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Dirk Kostrewa wrote:
> 
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> On Friday 15 November 2002 17:54, Gerard DVD Kleywegt wrote:
> > a model deposited without data (or not at all) one has to take on faith
> > (i.e., more religion than science). for a model deposited with data, you
> > can go and check the electron density yourself (e.g., using the uppsala
> > electron density server, EDS, a pre-release version of which is available
> > at
> > http://fsrv1.bmc.uu.se/eds).
> 
> On Friday 15 November 2002 19:06, Phil Evans wrote:
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> >
> > On the question of depositing structure factors, this should be
> > compulsory (why isn't it?). There is no excuse for not depositing
> > them, and the most likely person to want them is you yourself.
> 
> Dear Gerard and Phil,
> 
> I think that in addition to deposit observed structure factors there is also a
> need to deposit the calculated structure factors _exactly_ as they came out
> of the scaling/refinement for the reported R-factors of the model. The reason
> for this is that if somebody takes the deposited model and the deposited
> observed structure factors and does not apply the proper anisotropic scaling,
> bulk solvent correction and weighting, the difference map will show features
> that are not consistent with the model. For that reason, personally, I still
> hesitate to publish observed structure factors until I can easily deposit the
> calculated structure factors and their phases _along_ with them. In
> principle, agree with both of you that these are data that should be
> published, but I must admit that I shy away from this until I can easily
> publish all the data.
> 
> Best regards,
> 
> Dirk.
> 
> --


 Not sure what the problem is? I thought it was the default?, and maybe
even a requirement to deposit calculated SFs? If you follow the standard
mmCIF output you get the Fcs and PHICs as well as the observed data. 
What is done with the information is up to the community - those who
have map generating programs prob also have structure factor routines
and it is often more informative to recalculate maps for a range of
molecules in a standard way.. Most people are not going to use such data
for ultra-careful analysis of finest details of the maps!

Also to use someone elses SFs for comparison requires that a LOT of
information is deposited - how was it scaled? how  were the Free
reflections handled? etc etc which I dont think is properlay formulated
at deposition..

 Eleanor

I agree with Tassos it is not really essential - for instance if you
want to check ligand density wou would have to recalculate the structure
factors without the ligand included..



 

> 
> ****************************************
> Dirk Kostrewa
> Paul Scherrer Institut
> Life Sciences, OSRA/007
> CH-5232 Villigen PSI, Switzerland
> E-mail: dirk.kostrewa@psi.ch
> Phone: +41-56-310-4722
> Fax: +41-56-310-4556
> WWW: http://www.sb.psi.ch
> ****************************************

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Eleanor J.Dodson, York Structural Biology Laboratory,
                  Chemistry Department, 
                  University of York, Y01 5DD Heslington, U.K.
Tel: Work: +44 (1904) 32 82 53  Home +44 (1904) 42 44 49
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