[phenixbb] Real space refinement

Pavel Afonine pafonine at lbl.gov
Sun Feb 16 23:28:03 PST 2014

Hi Mavis,

you can do it in Phenix. Command line tool for this is: 
phenix.real_space_refine. Just give it map and model and see what 
happens, like this:

phenix.real_space_refine model.pdb ccp4_formatted_map.map

I wrote this program specifically to do various kinds of model 
refinement against the map, with the main focus on EM maps. Have a look 
at the article that briefly describes it here:
"New tool: phenix.real_space_refine".
The article is from last year but I haven't done much since then so it 
pretty much documents the current state of the art.

Should you have any questions or problems or need any help with this 
please let me know off list.

All the best,

On 2/14/14, 8:45 AM, Agbandje-Mckenna,Mavis wrote:
> Dear Pavel,
> I don't believe we have met, but you have received several e-mails from people in my group (including Sujata (Tina) Halder) and also helped them with their use of Phenix - thank you.
> I have a question for you regarding real space refinement in Phenix.  We have a 3.7 Angs cryo-EM reconstructed structure for a virus capsid and we have been able to build a model for the capsid VP using COOT.  I would like to refine this model further against the map using real space refinement.  I am trying to find a suitable program that would allow me to do this.  I believe Phenix can do it, but I am not sure.  Could you give me some direction?
> Thanks in advance.
> Best wishes
> Mavis
> Mavis Agbandje-McKenna, Ph.D.
> Director, Center for Structural Biology
> Professor, Dept. of Biochemistry and Molecular Biology
> Center for Structural Biology
> The McKnight Brain Institute
> P.O. Box 100245 Tel.: 1-352-392-5694
> University of Florida Fax.: 1-352-392-3422
> Gainesville, FL 32610-0245 e-mail: mckenna at ufl.edu
> Website: http://msg.mbi.ufl.edu

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