Sorry a bit late, but I like to briefly comment, since it was me who
changed it...
> I find the coot NCS map facility is enough for my requirements.
> I sometimes do the COOT fit model for all chains to get the best fit at
> this point; do some cycles of refinement for the improved model, then
> read back coordinates and map and let the NCS map calculation get an
> average map. I think the fit is based on SSM matching of the coordinates?
> Paul - is that right?
Not for some time. Currently the default is LSQ to speed up things for
multiple and/or large NCS copies. However, you can change it back to SSM
for more accuracy in case of badly matching NCS copies or even speed it
up more by using less atoms for the LSW fit:
Extensions->NCS->NCS Matrix type (*)
Bernhard
(*) Note so self: should be a radio menu item ... FIXME
> Eleanor
>
> On 4 March 2016 at 14:46, Randy Read <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Dear Zachary,
>
> In the CCP4 suite, I'm pretty sure both parrot and dmmulti refine
> the NCS operators, and the averaging tools in the Phenix suite do as
> well.
>
> Best wishes,
>
> Randy Read
>
> > On 4 Mar 2016, at 13:44, Zachary A. Wood <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
> >
> > Hello All,
> >
> > Does anyone know of any ‘newer’ programs that do what Kleywegt’s
> wonderful RAVE software package does?
> >
> > What is great about RAVE is that you generate a mask based on the
> coordinates of a protomer, you then optimize your NCS operators
> using the masked electron correlation coefficients of the other
> protomers, and then generate a nice, averaged electron density map
> for model building. The electron density based optimization of the
> NCS operators is the best feature in my opinion. I am hoping that
> someone has automated this process of electron density averaging.
> Don’t get me wrong, RAVE does a fantastic job, but it is a bit time
> consuming and seems ripe for some automation (especially when
> teaching undergrads how to do this stuff). Thanks in advance for
> any suggestions.
> >
> >
> > Best regards,
> >
> > Z
> >
> >
> > ***********************************************
> > Zachary A. Wood, Ph.D.
> > Associate Professor
> > Department of Biochemistry & Molecular Biology
> > University of Georgia
> > Life Sciences Building, Rm A426B
> > 120 Green Street
> > Athens, GA 30602-7229
> > Office: 706-583-0304 <tel:706-583-0304>
> > Lab: 706-583-0303 <tel:706-583-0303>
> > FAX: 706-542-1738 <tel:706-542-1738>
> > ***********************************************
>
> ------
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: + 44 1223 336500
> <tel:%2B%2044%201223%20336500>
> Wellcome Trust/MRC Building Fax: + 44 1223 336827
> <tel:%2B%2044%201223%20336827>
> Hills Road E-mail:
> [log in to unmask] <mailto:[log in to unmask]>
> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
> <http://www-structmed.cimr.cam.ac.uk>
>
>
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