rigid fitting into EM density maps in IMP
Dear IMP dev,
In the sake of transparency and collaboration I wanted to give everyone an update on the work we have been doing on em fitting. We will try to send these updates to everyone from time to time so the work being done is fully transparent and clear. The recent efforts can be divided to two main categories: 1. scoring We worked with Daniel and Ben on various code optimization that now allow for even faster rigid body scoring. Specifically, the model simulated map is resampled only once and for the rest of the transformations the resampled map is transformed. We are also now able to apply the same idea to multiple rigid bodies, as we found a way to decompose the CC score into rigid terms, while still maintaining the correct combined score. Examples can be found in the test can examples directories on the em module. 2. optimization We have developed 4 rigid fitting procedures: (i) MC/CG local refinement, (ii) principal component based rigid fitting, (iii) fft based rigid fitting and (iv) anchor points based rigid fitting. (i) and (ii) are fully integrated into IMP, while (iii) and (iv) require external libraries (fftw3 and gamb), and are now in the process of being merged into IMP with Ben's help. Examples can be found in the test can examples directories on the em and multifit modules.
Current usages of the new code were quite successful. Charles used it to fit 1000 proteins into more than 5000 maps and all went well. In addition, we tested the new code on a large benchmark of protein assemblies and were able to get accurate fits.
As we are in the process of making all publicly available in IMP 1.1 and currently writing a tutorial on the em module in IMP, we will be happy to get specific feedback, comments or ideas for improvements.
thanks, Keren.
it'd be great if all developers were updating us like this. thanks, andrej
On Sep 12, 2010, at 8:14 PM, Keren Lasker wrote:
> Dear IMP dev, > > In the sake of transparency and collaboration I wanted to give > everyone an update on the work we have been doing on em fitting. > We will try to send these updates to everyone from time to time so the > work being done is fully transparent and clear. > The recent efforts can be divided to two main categories: > 1. scoring > We worked with Daniel and Ben on various code optimization that now > allow for even faster rigid body scoring. Specifically, the model > simulated map is resampled only once and for the rest of the > transformations the resampled map is transformed. We are also now able > to apply the same idea to multiple rigid bodies, as we found a way to > decompose the CC score into rigid terms, while still maintaining the > correct combined score. Examples can be found in the test can examples > directories on the em module. > 2. optimization > We have developed 4 rigid fitting procedures: (i) MC/CG local > refinement, (ii) principal component based rigid fitting, (iii) fft > based rigid fitting and (iv) anchor points based rigid fitting. > (i) and (ii) are fully integrated into IMP, while (iii) and (iv) > require external libraries (fftw3 and gamb), and are now in the > process of being merged into IMP with Ben's help. Examples can be > found in the test can examples directories on the em and multifit > modules. > > Current usages of the new code were quite successful. Charles used it > to fit 1000 proteins into more than 5000 maps and all went well. In > addition, we tested the new code on a large benchmark of protein > assemblies and were able to get accurate fits. > > As we are in the process of making all publicly available in IMP 1.1 > and currently writing a tutorial on the em module in IMP, we will be > happy to get specific feedback, comments or ideas for improvements. > > thanks, > Keren. > > > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary@salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali@salilab.org; Web http://salilab.org
participants (2)
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Andrej Sali -
Keren Lasker