Xplor3.843 map.

[chenlong at BIO.CORNELL.EDU]

Dear X-plorers,

I'm refining a complex structure using Xplor3.843. There are clear substrate 
densities in fo-fc map. However,if I put the substrate models into the 
densitiesand after one round of slowcooling I calculate fo-fc map again this 
time with substrate models in the overall model. I find there are big,messy 
positive density(>3*sigma) and well shaped big negative density blobs(>3*sigma) 
around the substrate models.

I'm aware that it's substrate not inhibitor and soaked not co-crystallized,so 
the substrate may have low occupancies and may adopt more than one conformer 
struceures in the active sites. But I'm still puzzled by the messy densities 
resulting from the insertion of the models. 

I got almost the same results whether I choose the sigmaa_flag true or false. 
And without substrate model the scale R=0.22 and with substrate model the scale 
R=0.36.looks quite big a difference.

Hope some experts can point me out the problem. And also how can I get the 
xplor3.1 map without excessive memory usage? Thanks very much.

Chenlong Li
Ealick lab
chenlong at bio.cornell.edu