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Re: [ccp4bb] Problem on creating a new monomer
 

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CCP4bb <-- 2007 <-- May 2007 <-- 07 May 2007
Previous message:
Subject: Alternate space groups for MR in Beast
From: "Edward A {- dot -} Berry" EABerry {- at -} LBL {- dot -} GOV
Date: 2007-05-07 		Next message:
Subject: Re: Alternate space groups for MR in Beast
From: "Das, Debanu" debanu {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-05-07


Subject: Re: Problem on creating a new monomer
From: artis {- at -} CHEMISTRY {- dot -} MONTANA {- dot -} EDU artis {- at -} CHEMISTRY {- dot -} MONTANA {- dot -} EDU
Date: 2007-05-07
Hi XJXJ,
Did you create a library for this yourself? If you fix the ligand into the
density and use those coordinates to create a monomer library for it in
refmac, and use this during refinement, it might let it stay that way.
Arti

> Hi there,
> 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?
>
> Thanks a lot!
> Xiaofei
>
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Arti S. Pandey
Graduate Student
Chemistry and Biochemistry
Montana State University
Bozeman,MT 59717

CCP4bb navigation

CCP4bb <-- 2007 <-- May 2007 <-- 07 May 2007
Previous message:
Subject: Alternate space groups for MR in Beast
From: "Edward A {- dot -} Berry" EABerry {- at -} LBL {- dot -} GOV
Date: 2007-05-07 		Next message:
Subject: Re: Alternate space groups for MR in Beast
From: "Das, Debanu" debanu {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-05-07


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