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[ccp4bb] Thanks! Re: [ccp4bb] Problem on creating a new monomer
 

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CCP4bb <-- 2007 <-- May 2007 <-- 07 May 2007
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Date: 2007-05-08


Subject: Thanks! Re: Problem on creating a new monomer
From: XJ XJ nesky_jia {- at -} YAHOO {- dot -} COM {- dot -} CN
Date: 2007-05-07
Thanks for all the quick replies! The problem turned
out to be that the Turbo output pdb file of my ligand
(created by using the MAKE command) somehow failed to
label all my carbon atoms as "C". Instead, all my
carbons were labelled with just the number. For
example, C12 was mislabelled as 12. After I put "C"s
back to where they should be, everything went ok.
Now, after several refinement runs, the ligand is
sitting very comfortably in the density:D. Thanks for
all the timely help! Have a great one!
Regards,
Xiaofei

--- Kendall Nettles wrote:

> 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
> > Reply-To: XJ XJ
> > Date: Mon, 7 May 2007 11:05:52 -0700
> > To:
> > 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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