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.
