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Paul, The same problem is caused by isoaspartate modifications, which I wrote to you about a few months ago. There, you have ----RNH--CO--CH2--CHR--NH----- a linker with a CH2 group inserted into the chain. Apparently quite a few proteins undergo this sort of isomerisation, but people usually assume the electron density is disordered... I still do not know how to model it for one of my structures in COOT. See residue IAS101 in 1at6, for example... Tadeusz "Paul Emsley" <[log in to unmask]> Sent by: "Mailing list for users of COOT Crystallographic Software" <[log in to unmask]> 15-May-2007 10:59 Please respond to "Mailing list for users of COOT Crystallographic Software" <[log in to unmask]> To [log in to unmask] cc Subject Re: [COOT] inter-residue restraints On Tue, 2007-05-15 at 17:06 +0800, Charlie Bond wrote: > > > Coot uses the _chem_comp.group to determine the link type. > > It needs to be either L-peptide or D-peptide to be linked as an amino > > acidic chain. > > How about non-peptide links, of which my molecule contains a number (15 > or so, see PDB 1E9W for an example)? 1E9W: Yikes! I think I'll use that as a torture test for the forthcoming LINK code. I can't help at the moment, sorry. This will be fixed along with glycosylation and branching carbohydrates. Paul. ----------------------------------------------------------- This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. -----------------------------------------------------------