On 09/02/2021 07:10, Arunabh Athreya wrote:
Hi
I have been facing a similar problem with a backbone thiocarbonylated
L-serine residue (here's the SMILES: N[C@@H](CO)C(O)=S )
This residue was not present in the pre-existing library, so I did the
following:
1. Used AceDRG to draw the structure of the residue; saved the
restraints and coordinates as XSR.cif and XSR.pdb.
2. Opened protein pdb and mtz files in coot and centred on the
residue that I had to mutate (*chain A residue 104 SER (the
residues are numbered from 101 to 122) *)
3. File -> import CIF dictionary -> XSR.cif (generate a molecule
activated).
4. Edit -> Change Chain IDs -> (Using residue selection 'whole chain'
of XSR.pdb) to "A".
5. Edit -> merge molecules -> XSR.pdb and protein.pdb to protein.pdb.
XSR got renumbered as 201.
6. Edit -> renumber residues -> residue 201 -> apply offset by -97.
Once this was done, the bonds were automatically formed at desired places.
The problem came up when I tried to use real space refine zone. The
residue 104 ejected from its electron density, and even if I do/don't
do it, refmac crashes afterwards.
I cannot figure out why Refmac crashes when I insert this XSR residue
but works ok with all other residues.
1: AceDRG doesn't do drawing, perhaps you meant Lidia
2: Your SMILES is non-optimal - you need to include the carboxylate, not
an implicitly linked carbonyl, i.e. NC(C(=O)O)C(O)=S
3: $ pyrogen -n 'NC(C(=O)O)C(O)=S'
4: $ acedrg -c XSR-pyrogen.cif -p -o XSR-acedrg
5: hand edit XSR-acedrg.cif: replace non-polymer with L-peptide, replace
all O1 by O
6: In Coot, File -> read CIF dictionary -> XSR-acedrg.cif
7: In Coot, centre on the SER that you wish to modify
8: In Coot, Calculate -> Modelling -> Replace Residue -> XSR
9: Refmac doesn't crash it refuses to proceed with an inconsistency
between the model and the dictionary.
Paul.
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