[phenixbb] Real space refinement

[Pavel Afonine]

Hi Mavis,

there are two options.

One is convert your EM map into structure factors Fobs and HL 
coefficients using phenix.map_to_structure_factors command and then use 
phenix.refine to do reciprocal space refinement. This is somewhat 
indirect way. The good thing about it is that phenix.refine has a broad 
range of tools to handle low resolution refinement.

Another option is to use phenix.real_space_refine to refine model 
against the map directly. This is a preferred way but 
phenix.real_space_refine is new, less mature program and it generally is 
still under development (though it's functional if you try it now). So 
if it does not work as you expected or you have any feature requests or 
any questions or any other feedback - please do not hesitate to let me 
know, as this may help to improve this tool.

All the best,
Pavel


On 2/17/14, 6:14 AM, Agbandje-Mckenna,Mavis wrote:
> Dear Pavel,
>
> Thank you so much for getting back to me - this is much appreciated.  We received a script from Hong Zhou's group who have been using Phenix to refine the model for their 3.3 Angs cryo-EM Aquareovirus structure that we were going to try but this seems a lot more simpler!
>
> Thanks again.  I will let you know how it turns out.
>
> And thank you for the attached pdf.
>
> 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
> ________________________________________
> From: Pavel Afonine [pafonine at lbl.gov]
> Sent: Monday, February 17, 2014 2:28 AM
> To: Agbandje-Mckenna,Mavis; phenixbb at phenix-online.org
> Cc: Lins, Bridget; Drouin,Lauren M
> Subject: Re: Real space refinement
>
> 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:
> http://www.phenix-online.org/newsletter/CCN_2013_07.pdf
> "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,
> Pavel
>
> 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