Are you using TLS? If so the B factors in the PDB file are relative to
the TLS parameters..
Or have you lost low resolution data - you can see that in many plots -
one in REFMAC gives <F> v <Fcalc> as a function of resolution?
If so you probably need to use SCALE SIMPLE - in gfact that is usually
the safest option..
Which version of CCP4 are you using?
Eleanor
German Gomez wrote:
I am working with a small protein in a relatively high
space group p6322 and have good data to a modest 2.5 A
resolution. During the first rounds of restrained
refinement however the B factors drop to an average of
15 and as low as 2 A^3. This has the effect of
producing large amounts of negative density in the
voids of the structure. I have tried artificially
rasing the b factors and setting a higher low cutoff
but nothing seems to help. I have also chosen each of
the b models of refinement (anisotropic, overall,
etc.) but to no avail.
Any suggestions?
German Gomez
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