You can define an UNL (unknown ligand) in the blob. This is the standard name for such a
compound. It becomes a bit messy in refinement in terms of restraints, but it does exactly
what you want it to do: say you noticed the blob but couldn't figure out what it was.
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Dom Bellini
> Sent: Sunday, June 14, 2015 11:36
> To: [log in to unmask]
> Subject: Re: [ccp4bb] Residual density feature
> Dear Colin,
> I believe people usually refer to it as "unidentified blob" when depositing/writing in
> cases. But I wonder whether others may suggest better options.
> From: CCP4 bulletin board [[log in to unmask]] on behalf of Colin Levy
> [[log in to unmask]]
> Sent: 14 June 2015 09:53
> To: ccp4bb
> Subject: [ccp4bb] Residual density feature
> Dear all,
> I am currently working on a structure that contains a residual density feature located
> the active site. Due to a combination of factors including limited occupancy, modest
> resolution, twinning etc it has not been possible to unambiguously identify this feature
> fairly extensive efforts.
> What is the best way of dealing with such a feature when depositing the structure?
> would like to draw attention to the presence of residual density whilst not implying
that I have
> been able to identify it.
> Many thanks,
> Dr. Colin W. Levy
> MIB G034
> Tel. 0161 275 5090
> Mob.07786 197 554
> [log in to unmask]<mailto:[log in to unmask]>
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