Yes, rigid body refinement works great, but your assumption that a model
already exists does not apply in most situations where people are using
NCS averaging.
Cheers,
On 03/04/16 08:59, Tim Gruene wrote:
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> Dear Z,
>
> naively I would think that rigid body refinement, maybe with ncsr switched on
> in refmac, is similar if not superior to improving NCS operators based on the
> density. Then you can click on Calculate->NCS map in coot after you read in
> the PDB file.
>
> Best,
> Tim
>
> On Friday, March 04, 2016 01:44:00 PM Zachary A. Wood 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
>> Lab: 706-583-0303
>> FAX: 706-542-1738
>> ***********************************************
> - --
> - --
> Paul Scherrer Institut
> Tim Gruene
> - - persoenlich -
> OFLC/102
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5754
>
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All Things Serve the Beam
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David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
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