[Chimera-users] related with Fit in map option

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 29 15:42:44 PDT 2014

Hi Srdja,
I am no EM expert, but my best guess is that this is a scientific judgement call.  In other words, there is no specific correlation number or statistic (or difference when comparing two possibilities) that allows you to state definitively that a map matches a certain conformation.  For example, the map might represent some other conformation that isn't exactly like either of the atomic structures.The fitting statistics are additional pieces of evidence that could be combined with other knowledge to reach a conclusion of what is most probable.

Perhaps others who actually work with EM data will have an opinion, however.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 29, 2014, at 3:49 AM, "SRDA.DRAKULIC.599589" <sdrakulic at cib.csic.es> wrote:

> Hi,
> I have a question related to Fit in Map option and how to evaluate subsequently given results. I have a EM map at 19 ang. resolution of protein at yet non-characterised activity state, and there are two atomic structures of homologue of that protein, at clenched and open, active state. I would like to relate that state to one of the atomic structures, thus, both of them were fitted in my EM map and for the clenched state I got following values:
> cross correlation: 0.8447;
> average map value 9.526;
> and number of atoms outside the contour: 1709/7621 (or 22.42%)
> For the open state:
> cross correlation: 0.8385;
> average map value 9.085;
> and number of atoms outside the contour: 2064/8124 (or 25.42%)
> Are those differences big enough to say with certainty that my protein is at  conformation similar to the clenched one or due to the EM map resolution this can not be said.
> Sincerely,
> Srdja Drakulic

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