[Chimera-users] related with Fit in map option

Tom Goddard goddard at sonic.net
Tue Apr 29 17:06:36 PDT 2014

Hi Srdja,

  I agree with Elaine that these small differences in correlation are not strong evidence.  You should look at where the molecular models fail to match to the EM map to get a better understanding.  You can make a simulated map from each molecular model and do a local correlation coloring to see where the differences are.


Or maybe better for seeing the differences you could morph between the experimental map and simulated molecule maps.


You’ll need to resample the simulated map (made with molmap) on the grid of the experimental map, so both maps have the same grid to do this
(e.g. "vop resample #1 ongrid #0” where #1 is the simulated map and #0 the experimental map).


On Apr 29, 2014, at 3:42 PM, Elaine Meng wrote:

> 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.
> Best,
> Elaine
> ----------
> 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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