Paul Emsley wrote:
Ian Tickle wrote:
All - can anyone help me with the syntax of the 'mutate_by_overlap'
scripting command. I need to mutate a CYS to a chemically-modified
entity that I've called CYD. I made a Refmac dictionary entry for
this which I read in & it's accepted. I'm using WinCoot so I
understand I must use Python syntax.
I've tried the following:
mutate_by_overlap(0,"A",17,"CYD")
That's what I would have used.
Additional thoughts:
The Manual for this is wrong. There is a GUI interface: Extensions ->
Modelling -> Replace Residue
However, coot does not think about what it has loaded when doing
mutate_by_overlap - so even if you replaced with an ALA, it would go off
and ask libcheck/refmac to make an ALA.
If you have used mutate_by_overlap or get_monomer previously and if it
can find them, coot will use monomer-XXX.pdb and libhcheck_XXX.cif on
disk rather than run libcheck/refmac (see recent correspondence with
Frank about this).
I can see now that if you have already loaded a molecule with a single
residue with name XXX and you have read in a dictionary entry for XXX,
then coot should use that.
Paul.
