Dear Paul, I see. Even with imported IAS cif, if I do real space refinement of the IAS and the next amino acid to IAS, Coot always pushed away the peptide link out of electron density, this may be due to the "CG-linking" problem as you mentioned.
Thank you very much for the information. Regards, Xiao On Sat, Dec 30, 2017 at 5:38 PM, Paul Emsley <[email protected]> wrote: > On 30/12/2017 19:32, Xiao Lei wrote: > >> Dear All, >> >> I am using WinCoot 0.8.6.1 . >> > > :-/ > > >> I find Coot fails every time when doing real space refinement of >> Iso-aspartic acid residue (IAS) in PDB entries containing IAS. >> >> For example, in PDB entry 1DY5 chain A residue 67th IAS, when doing real >> space refinement of this residue, Coot fails with error message "Refinement >> setup failure, Failed to find restraints for: IAS". >> >> To import the IAS cif file, I tried to get monomer in Coot File---> Get >> monomer.. , input IAS, but Coot fails with message "We don't have the entry >> for this. Shall I go and get it?" After I click ok, Coot fails with message >> "Failed to import molecule." >> > > As I am sure that you know, IAS is an unusual amino acid - it doesn't form > standard peptide links, instead it make a bond between the CG of the > "side-chain" and the N of the next residue. Poor old Coot doesn't know how > to do CG-linking. > > >> As far as I tried, this problem occurs at other entries containing IAS in >> PDB (for example entry 1RTU chain A 45th IAS). >> >> I am asking if any of you have some suggestions of doing this. >> > > The trivial problem you mention above - about importing the molecule I > will certainly fix (that will take an hour or so). But the real problem - > "CG-linking" will take a long time - and is not scheduled. I'll add it to > the todo list for 0.9. > > In the mean-time you can use Acedrg in "link-building" mode (-L) and > import the resulting dictionary into Coot - that may work (not tried). > > Regards, > > Paul. > > >
