RE: [ccp4bb]: Refmac vs. cns with NCS

[Kostrewa Dirk <dirk.kostrewa@psi.ch>]

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> -----Original Message-----
> From: David J. Schuller [mailto:djs63@cornell.edu]
> Sent: Montag, 21. Januar 2002 17:30
> To: rams@poori.biochem.uiowa.edu
> Cc: ccp4bb@dl.ac.uk
> Subject: Re: [ccp4bb]: Refmac vs. cns with NCS
> 
> i am not entirely satisfied with NCS under CNS.  you have a 
> choice between 
> strict NCS (constraints) or NCS restraints. if you want to 
> switch from one 
> to the other, you have to build a new coordinates file and 
> then re-run 
> generate.  this is a nuisance.  and in both cases, the NCS is 
> constrained/restrained by the NCS matrix, which itself is not 
> refined. to 
> do that, you have to build the whole multimer and put it 
> through rigid 
> body fitting.  why not allow the NCS matrix to be refined 
> with either/or 
> constraints & restraints?

I still think, that TNT (5F) is one of the most elegant and transparent
refinement packages if it only had a good implementation of the maximum
likelihood target (the one from Navraj Pannu works in principle but it
didn't write out sigmaa-weighted electron density maps; BUSTER/TNT is an
attractive alternative, but it is still in the development phase).
Especially for NCS, you can define in TNT 5F simultaneously constraints and
restraints in the refinement protocol, and it is the only program that
allows to use different B-factor levels for the individual protomers! We
probably have all noticed that multiple copies not necessarily are equally
well ordered. 
During the course of refinement/model building I usually do once a
comparison between TNT, BUSTER, REFMAC, and CNS: TNT performs still very
well (but least-squares, only), BUSTER produces sometimes astonishing
electron density maps for questionable regions, REFMAC and CNS both perform
very well and are good for the daily refinement jobs. I agree with Bart,
that in CNS both the scripts themself and the scripting language became too
complicated to be modified by myself.

Regards,

Dirk.


*****************************************************
Dirk Kostrewa
Paul Scherrer Institut   e-mail: dirk.kostrewa@psi.ch
Life Sciences             phone: +41-56-310-4722
OSRA/007                    fax: +41-56-310-4556
CH-5232 Villigen PSI        WWW: http://sb.web.psi.ch
Switzerland
*****************************************************


> -----Original Message-----
> From: David J. Schuller [mailto:djs63@cornell.edu]
> Sent: Montag, 21. Januar 2002 17:30
> To: rams@poori.biochem.uiowa.edu
> Cc: ccp4bb@dl.ac.uk
> Subject: Re: [ccp4bb]: Refmac vs. cns with NCS
> 
> 
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> On Mon, 21 Jan 2002 rams@poori.biochem.uiowa.edu wrote:
> 
> > REfmac Vs CNS.
> > CNS, simulated annealing and
> > water picking do an absoltely wonderful job with strict NCS.
> 
> i am not entirely satisfied with NCS under CNS.  you have a 
> choice between 
> strict NCS (constraints) or NCS restraints. if you want to 
> switch from one 
> to the other, you have to build a new coordinates file and 
> then re-run 
> generate.  this is a nuisance.  and in both cases, the NCS is 
> constrained/restrained by the NCS matrix, which itself is not 
> refined. to 
> do that, you have to build the whole multimer and put it 
> through rigid 
> body fitting.  why not allow the NCS matrix to be refined 
> with either/or 
> constraints & restraints?
> 
> and to bring in a dark horse, SHELX has a different approach 
> to NCS which 
> makes a lot of sense to me. NCS restraints are applied not to 
> the position 
> as defined by the NCS matrix, but by extra restraints on 
> torsional angles. 
> this is particularly appropriate for structures with hinges or other 
> localized differences between monomers.
> 
> cheers,
> ==============================================================
> =========
> "Now that I'm a cranky, constipated old man I can afford to say that
>  the younger generation of scientists makes me sick to my stomach."
>                                                   - C.M. Kornbluth
> ==============================================================
> =========
>                         David J. Schuller
>                         modern man in a post-modern world
>                         MacCHESS, Cornell University
>                         djs63@cornell.edu
>