Dear Drew,

   Your loop region might or might not obey the ncs of the rest of the
molecule, so you should be sure to examine both the ncs averaged map
and each individual, nonaveraged, map.

   You should be willing to accept, however, that this region may not
structured and it may not be possible to build a single model in any
of the individual maps.  The model you build has to be justified by
the map before you build it.  It is not uncommon for a portion of a
binding site to be disordered in the absence of its ligand.

   Soaking the ligand into a crystal and collecting new data might
be more useful than spending time staring at blobs.

Dale Tronrud

Drew Waight wrote:
> Hello all,
> 
>       I'm just finishing up my first structure, a membrane protein with 5
> fold NCS. The native dataset is good to about 2.1A. The R factors are good,
> around .22/.26 without waters. The only problem is that I'm having a
> difficult time fitting what looks to be a very important (potential binding
> site) loop region of about 20 AA or so because the density is poor. I have
> relied heavily on the NCS to solve the rest of the structure, but releasing
> the constraints doesn't particularily help. I can see green blobs here and
> there in the difference map, and there is some continuous density at .8
> sigma but its much poorer than the rest of the protein. (which is also
> mostly alpha helical) I would imagine that this is a common problem and am
> wondering if there are any tips from the experts seeing as I am extremely
> new to this. Thank you all, I have already learned a great deal from this 
> board.
> 
>                                                                     Drew
> 
> P.S. I have been using CCP4, Coot, Refmac, DM, Resolve (for dm), and Phenix
> refine

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