I wish I could answer this!
One possibility is that the side-chain B values are too tightly
restrained - Ian Tickle recommends releasing these somewhat..
Here are the default refmac values.
THERMAL FACTORS
Weight= 1.00
Main chain bond (1-2 neighbour) 1.5A**2
Main chain angle (1-3 neighbour) 2.0A**2
Side chain bond 3.0A**2
Side chain angle 4.5A**2
and you could change them say to:
Under GUI - check geometric parameters and alter the Bfactor values
data line becomes: temp 1.0 1.5 2.0 4.0 6.0
The trouble is that resyraints for ARG or MET say should be looser than
those for SER or VAL.
But I often finish up with some inexplicable red blobs - sometimes
floating in space..
Eleanor
On 11/23/2011 08:39 AM, DUFF, Anthony wrote:
Delete (set occupancies to zero) the side chain back to CA. Do a few rounds of
refinement and calculate Fo-Fc and examine.
It is possible that the side chain is disordered, or ordered in multiple
conformations. Compare the density for alternate confonformers against the
density for CA.
Alternatively, your side chain B-factor restaints might be too tight.
Anthony
________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Careina Edgooms
[careinaedgo...@yahoo.com]
Sent: Wednesday, 23 November 2011 6:54 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] negative density in difference map
Good morning CCP4 members
I have a question about a 2F0-Fc difference map that I calculated with Refmac.
In some instances it gives me negative (red) density around part of a side
chain and no positive density in sight. Furthermore the entire residue fits
well into the blue density of the complete map, including the part with
negative density.
I am struggling to interpret this. Does the fact that it fits the blue density
mean that the side chain is in the correct place or does the red blob on part
of the side chain (eg on the sulphur in a Met residue) mean that something
funky is happening with this side chain?
Thanks for any assistance
Careina
