Karen and all,I don't really know the answers to your questions, but I have been making new residues by defining a new residue type, as described in the FAQ. I have also left them as HETATMs, but I'm not sure that is the best thing to do. The Swiss pdb viewer connects the atoms together ( and sometimes it connects some I don't want connected). In Hyperchem, the atoms must either be connected by hand, or by a set of CONECT statements in the pdb file. I also would like to know if this is the best way to do it. I have been adding big fluorescent residues, and it is impossible to restrict them so that they remain flat. They start out OK, but get a bit bent in the course of making a model. I've defined a lot of impropers; does any one know how to get a polycyclic ring to stay flat? I posted an example of my attempts earlier.
John Penniston Modeller Care wrote:
forwarded by the list owner ------------------------------------------------------------------ Dear All, My question is regarding the modelling of modified protein residues (i.e. phosphotyrosine: PTR). I know the restype.lib and Modeler libraries contain defintions for some modified residues (e.g selenomethionine) but will not contain them all. For cases like PTR, is it best to define my own residue type within the Modeler libraries or is there a simpler method? Also, I have query as to the accepted way of dealing with the format of modified residues in PDB files. In PDB files, modified residues are defined within the ATOM coordinates in the correct sequence position but labelled HETATM. I assume its ok to leave them in this format? Does Modeler read them as actual atoms or do you need to change the labelling? My apologies if the answer to this question is rather obvious, I just want to make sure I'm using the accepted format for modified residues. Many thanks, Karen
-- John T. Penniston, Ph.D. Dept. of Biochemistry and Molecular Biology Guggenheim 16, Mayo Clinic 200 First St. SW Rochester, MN 55905 USA