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.
