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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 you would expect 2) read the REFMAC dictionary into coot and see what happens.. do you still have the problem. 3) check the REFMAC log file for what it thinks are outliers after the COOT refinement - I reset the geometric monitoring parameters - see on the GUI - to list things with errors of 5 Sigma say ( I think the default is 10 Sigma) 4) If there are difference complain.. Eleanor On 29 April 2012 10:14, H. Raaijmakers <[log in to unmask]> wrote: > 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 > > >