What I have been suggesting to the fine  EM people for a while, is to put in the correct scattering cross sections, and refine against phased structure factors in reciprocal space with R-free.  One could fairly easily weight phases more than amplitudes with one more tunable parameter.  Use R-free and this will get you most of the way there.  Seems this may be catching on a bit.

George

On Feb 17, 2014, at 9:33 PM, Pete Meyer <[email protected]> wrote:

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: [email protected]
Website: http://msg.mbi.ufl.edu
________________________________________
From: Pavel Afonine [[email protected]]
Sent: Monday, February 17, 2014 2:28 AM
To: Agbandje-Mckenna,Mavis; [email protected]
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: [email protected]
Website: http://msg.mbi.ufl.edu
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George N. Phillips, Jr.
Ralph and Dorothy Looney Professor
Department of Biochemistry and Cell Biology
Rice University, MS140
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Houston, Texas  77005-1892
Office: +1 713.348.6951
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