Re: [ccp4bb] Problem on creating a new monomer

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Alternate space groups for MR in Beast
From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-05-07

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Subject: Kabsch reference
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-05-07

Subject: Re: Problem on creating a new monomer
From: Kendall Nettles knettles {- at -} SCRIPPS {- dot -} EDU
Date: 2007-05-07

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?

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Alternate space groups for MR in Beast
From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-05-07

Next message:
Subject: Kabsch reference
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-05-07