You can renumber the residues within COOT. Calculate > Renumber Residue Input the residue numbers you wish to change, then by how many you want to offset the sequence.
I do not believe you should stick with 'standard numbering schemes'. It would probably be best (and make your refinement's easier) if you follow the actual numbering within your protein. Just my two cents. Any other suggestions about standard numbering nomenclature? Kelly Daughtry ******************************************************* Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548 ******************************************************* On Thu, Feb 25, 2010 at 8:12 AM, Vellieux Frederic <[email protected] > wrote: > Hi folks, > > I'm having a problem with Coot. Molecular Replacement solution to the phase > problem. The MR model has one small stretch of residues missing, for which > there is density in the maps (both normal and difference density maps). > Hence I have built the model into this density. Except that there is a > problem with the "standard" residue numbering scheme one has to use in this > class of enzymes. The numbering jumps from residue number 103 to residue > number 105. As a result, Coot won't accept that the residues be linked > together and forces them apart. The initial refinement round has corrected > this somewhat (but still not entirely, even though I had introduced a LINK > record in the PDB file before refinement). So I don't seem to be able to use > Coot to correct this. > > Hence the question: is there any way to force Coot to accept that these two > residues be connected together even though the numbering scheme is not > sequential? I haven't found the correct option anywhere. And I really do not > want to use a sequential numbering scheme for refinement and model building > only, since it would means plenty of residue number editing (by hand) to > re-introduce all of this weird residue numbering scheme, everywhere in the > subunit. > > Thanks, > > Fred. >
