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 [[log in to unmask]] on behalf of Careina Edgooms [[log in to unmask]]
Sent: Wednesday, 23 November 2011 6:54 PM
To: [log in to unmask]
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

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