Quasi on-topic rant:
I would advice against using the 'both' option for any well defined ligand.
It's a hack to avoid thinking about which atom belongs where and it allows you
to be inconsistent. This makes it difficult for others to use your model,
because aligning atoms of ligands becomes needlesly complicated. To the eye an
oxygen is an oxigen, to a computer O1 is different from O2. Just stick to the
definition given by the PDB (see Ligand Expo). It's there for a reason.
Cheers,
Robbie
> Date: Sun, 29 Apr 2012 11:14:01 +0200
> From: hraaijmak...@xs4all.nl
> Subject: Re: [ccp4bb] Ligand geometry
> To: CCP4BB@JISCMAIL.AC.UK
>
> Hmm, what are the perfect bonds, angles for NAD in your protein? remember
> that reactive groups can be in a "stressed" conformation, compared to
> ideal in vacuo conformations. As part of their functon.
> anyway, you'll have to check the restraints definition file (.cif). Bond
> lengths and angles are usually ok, but make sure only chiral atoms are
> defined as chiral, others need to be deleted or defined as "both".
> Check that the torsion angles make chemical sense, especially the
> "repetition factor" for rotatable bonds. Rotatable bonds next to aromatic
> rings are often problematic. You might need to set high sigmas, and
> "repetition" factors (x/360 degrees). On the other hand, you say that
> refmac behaves well, so the weighting scheme can't be far off.
>
> Cheers,
> Hans.
>
> And
> Uma Ratu schreef:
> > Dear All:
> >
> > I use Refmac5 to refine my model. After the run, I check the model quality
> > by Coot.
> >
> > Here is the problem:
> >
> > In Coot, the ligand - NAD, has bad geometry as indicated by a big red bar.
> > While the geometry of NAD fit nicely with the electron density.
> >
> > If I use refine tools (i.e. regularize Zone or real space refine zone),
> > the
> > geometry of NAD turns to perfec with bond, angle and so on. But the ligand
> > slightly turn away from the electron density map.
> >
> > If I run Refmac5 again with this modified model, the NAD turns back, fit
> > nice to electron density, but gives red bar in coot geometry.
> >
> > The Refinment Parameters in Refmac5 is set @ "use automatic weight" and
> > "use experinmental sigmals to weight X-ray terms".
> >
> > Thank you for advice and comments
> >
> > Ros
> >
