When refmac encounters a new ligand, it will fail, but also generate the
cif file for you. However, the library is often incorrect, and needs to be
carefully edited. Have you tried Coot for modeling? It handles ligands and
associated cif files quite nicely. You can also generate the cif file with
the Dundee PROGRG server, which is likely to be more accurate, as you can
specify the bond types.
http://davapc1.bioch.dundee.ac.uk/prodrg/
Kendall
> From: XJ XJ <[log in to unmask]>
> Reply-To: XJ XJ <[log in to unmask]>
> Date: Mon, 7 May 2007 11:05:52 -0700
> To: <[log in to unmask]>
> Subject: [ccp4bb] Problem on creating a new monomer
>
> I am trying to build a new ligand that I need to put
> into my structure. The problem I have right now is
> that, after regularising the molecule, a six-member
> ring always flip to the opposite orientation (the
> electron density map is defintely telling me which way
> the six-membered ring should go). I tried to fix it
> in turbo, but afterwards I cannot do refinememt of the
> fixed structure using refmac. The refmac log file
> said that all the atoms did not exist in the energetic
> library file---enre_lib.cif. Since this molecule is a
> totally new compound, I could not find anything close
> enough in the existing library. I'm now kind of stuck
> on this part. How can I get around this one?
> My other question is: are we not allowed to do much
> modifications to the ligand in turbo after we finished
> building and regularising it in the monomer sketcher?
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