Sounds like rad dam to me. See Burmeister, W. (2000)."Structural
changes in a cryo-cooled protein crystal owing to radiation damage",
Acta Cryst. D 56, 328-341. The first sign of a Met loosing its S-CH3
group will be a negative difference peak on the S.
-James Holton
MAD Scientist
On 11/22/2011 11:54 PM, Careina Edgooms wrote:
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
