[phenixbb] cif files
shyabiswas at gmail.com
Mon Jan 23 14:58:11 PST 2012
Thanks for your input, noticed that elbow does a better job with smiles
rather than pdb files.
On Sun, Jan 22, 2012 at 10:34 PM, Kendall Nettles <knettles at scripps.edu>wrote:
> I think prodrg used abc... etcetera to represent different atoms of the
> same element, while phenix uses numbers. You can hand edit this pretty
> easily, which is probably easier than editing the elbow produced cif to the
> correct geometry. However, it is also a good exercise to figure out how to
> hand correct the restraints at least one time. This is a common problem and
> we often try both elbow and prodrg, and sometimes neither will get it right
> for a complex ligand, so it is helpful to understand the restraint file.
> Kendall Nettles
> On Jan 22, 2012, at 9:36 PM, "Shya Biswas" <shyabiswas at gmail.com> wrote:
> > Hi all,
> > It appears that the cif file generated from prodrg (REFMAC format) is
> not recognised by phenix during refinement. Did anyone have similar issues
> or i am doing something wrong? somehow the geometries obtained from elbow
> are not right for my ligand so had to use prodrg to generate cif files.
> > thanks,
> > Shya
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