[phenixbb] Real space refinement

[Pete Meyer]

Pavel Afonine wrote:
> 
> 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.

Doing reciprocal space refinement for EM strikes me as something that 
might be problematic, at least from the theoretical sense.  The 
scattering factors going to Fcalc are assuming x-ray scattering, which 
might not be appropriate for an inverse-transformed EM map.  The 
weighting factors (Fobs:Fcalc agreement - not x-ray:geometry) assume 
that there's greater uncertainty in the phases than the amplitudes (at 
least as I understand it); for inverted EM the uncertainty for both 
components should be comparable.  Bulk solvent correction might also 
need to be tweaked (or disabled), but that's a less-fundamental issue.

That said, I have seen a couple papers where the authors refined against 
  an inverted EM map (and included R/Rfree and FOM statistics) that the 
reviewers must not have had any problems with.  So it's very possible 
that my impression is incorrect.



Pete

> 
> 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
> 
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