Hi,
Can't rotate the picture so that I can't see the distance between the
nitrogen and the green blob.
The green blob is elongated. Sometimes what happens is that you can have
2 waters (partial occupancies), in some unit cells in your crystals the
water occupies site 1, in the other unit cells the water occupies site
2. Obviously in the model you build, care should be taken during
refinement that these waters do not push each other away (VdW repulsion).
Anyway blobology is a difficult part of our trade.
Fred.
Fatima Fonseca wrote:
Dear CCP4BB users,
I have 2 questions:
I'm refining a very high-resolution structure (1.08 A) and I need help to solve a blob of positive density close to a modified Arg (N-omega-hydroxy-L-Arginine) - picture1. I tried to model a third conformation there but it didn't work - picture2.
In another protein model (1.35 Aº) I have a lot of positive peaks in the difference map that
I model as water molecules and after Refmac these "waters" have very high B
factors (>100 - 200) and appear as blobs of positive density. They make H bonds with 2-4
water molecules/protein residues within 2.66 - 3.0 A.
Any suggestions would be precious.
Fátima
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