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 > > >