CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> 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 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
