[Chimera-users] related with Fit in map option

SRDA.DRAKULIC.599589 sdrakulic at cib.csic.es
Tue Apr 29 03:49:28 PDT 2014


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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