CCP4 bulletin board <[log in to unmask]> wrote on 12/04/2008 02:50:30
PM:
> Thank you all for suggestions and explanations. I did not make it clear.
The
> tilt angle I wanted to restrain is the one from a C-OH bond to a plane
> (The C is in the plane). The O atom of OH group is not in the planar
> restraint in the cif file. At 2.1A I can "see" the feature of tilting of
> this OH group from the initial density map when the ligand was absent.
> But the density seems not strong enough to convince REFMAC that there is
> a tilt there. I have used very low weight term of 0.05 in the GUI to down
> weight the X-ray term. Refinement still pushed OH into the plane. I
wonder
> if there are other tricks that can impose the restraint for this torsion
> angle.
>
> Best,
> Huiying
Hi Huiying -
Before you spend more time adjusting your cif files, you should try
adjusting your refinement weight. As you said, you see a density feature
that's inconsistent with the standard protein geometry. If you down-weight
the X-ray term too much, all you will see in the final model is the
standard protein geometry enforced by the cif file. Try raising the
refinement weight to 0.08 or 0.1 and see if you can capture the
out-of-plane OH in your model without sacrificing your R factors or other
model geometry terms.
You should also look at the model to see *why* your OH is coming out of the
plane. Is there a steric clash pushing it, or a hydrogen bond pulling it?
If there is an H-bond, perhaps you need to adjust the position of the H
donor/acceptor so that Refmac recognizes the bond. Perhaps you need to
flip an Asn/Gln side chain so that the N and O switch positions?
Finally, re-reading your initial email, I see that this C-OH is in the
ligand. Did you create the cif file for this ligand yourself, or is this
in some standard dictionary? When I've made cif files for non-standard
ligands (using Refmac), I've observed that the algorithm tends to put
expand plane definitions (e.g. from conjugated ring systems) to include too
many neighboring atoms. I needed to trim the plane definitions and delete
a lot of inappropriate torsion angle restraints before my ligands would
refine correctly.
- Matt
--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116 fax:(212)645-2054
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