Hi Colin, 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.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Dom > Bellini > Sent: Sunday, June 14, 2015 11:36 > To: [email protected] > Subject: Re: [ccp4bb] Residual density feature > > Dear Colin, > > > > I believe people usually refer to it as "unidentified blob" when > depositing/writing in these > cases. But I wonder whether others may suggest better options. > > > > Best, > > > > D > > ________________________________ > From: CCP4 bulletin board [[email protected]] on behalf of Colin Levy > [[email protected]] > 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 within > 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 despite > fairly extensive efforts. > > What is the best way of dealing with such a feature when depositing the > structure? Ideally I > would like to draw attention to the presence of residual density whilst not > implying that I have > been able to identify it. > > Many thanks, > > Colin > > > Manchester > Protein > Structure > Facility > > Dr. Colin W. Levy > MIB G034 > Tel. 0161 275 5090 > Mob.07786 197 554 > [email protected]<mailto:[email protected]> > > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged > material, and are for the use of the intended addressee only. If you are not > the intended > addressee or an authorised recipient of the addressee please notify us of > receipt by returning > the e-mail and do not use, copy, retain, distribute or disclose the > information in or attached to > the e-mail. > Any opinions expressed within this e-mail are those of the individual and not necessarily of > Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from > viruses and we cannot accept liability for any damage which you may sustain > as a result of > software viruses which may be transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England and > Wales with > its registered office at Diamond House, Harwell Science and Innovation > Campus, Didcot, > Oxfordshire, OX11 0DE, United Kingdom
