Hi Uma,
How different are your NADs optimised in Refmac and Coot? Are you sure you are
using the same geometric restraints? Coot has to know where Refmac's restraint
files are. This info is passed through an environment setting on your computer
(I don't know the name by hart. Anyone?). Are you
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
I think you will find the dictionaries for coot and refmac are different..
REFMAC default dictionary will $CLIBD/monomers/n/NAD.cif
Good knows where coot finds its dictionaries - Paul?
1) check the REFMAC restraints in that dictionary are sensible - spec, are
the planes and chiral centres as
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
If the data set had P6 symmetry before anisotropic scaling it would
keep that symmetry afterwards. If it was only P2 symmetry before, it
certainly would not have P6 afterwards. Any anisotropic scaling I've
seen constrains the anisotropy to the lattice symmetry so symmetry
cannot be degraded
Hi Chen,
I see your point now. Yes, I agree that the 80:20 method (or 75:25 as stated
in the paper, http://www.mail-archive.com/ccp4bb@dl.ac.uk/msg01063.html) is
a very useful technique. The fact that it does not take much effort or lead
to uncertainties makes it very worth trying.
Here I
