Hi Mark, The issue here is that the dictionary does not define those atoms for e.g. ARG and GLN.
For ARG and GLN, the atoms bound to the CG are " HG1" and " HG2" - not Hx3. i.e. Coot doesn't know about bonds to those atoms, so it kicks them off with NBC restraints. By what means did you acquire those atoms? There may be a new convention about hydrogen naming that I don't know about... Paul. In message <[EMAIL PROTECTED]> Mark Collins <[EMAIL PROTECTED]> writes: > Hi Jonathan > Did you find/get a fix for this? I just switched to pdb v3 file, from the > happy and well behaved v2 file. It seems that all H_3 position Hydrogens > are the problem (ie HB3, HG3 etc.) and as descirbed fly off when using > RSR. > Thanks Mark > (os 10.4 G4, coot 0.5) > > > > > On Sun, 5 Oct 2008, Jonathan Winger wrote: > > > I'm building a structure in Coot 0.5. Upon real-space refine or > > regularize, some of the hydrogens on some residues fly off. It > > doesn't seem to be the old pdb v3 atom-name issue, since other > > residues in the structure with exactly the same atom names real-space > > refine without any trouble. Anyone have a fix for this? > > > > Any help would be greatly appreciated, > > Jon > >
