Karen Champagne wrote: > Hi All, > > I am having some trouble with a peptide ligand bound > to my protein. It is an 8-residue ligand and one of > the residues is post-translationally modified. > Because of this, when I load the model into O none of > the residues in the ligand are connected (i.e. no > peptide bonds). I am wondering how I can tell O to > connect all the residues? If I do 'make bond' between > them all it is fine at first, but after a round of > refinement the bonds are lost again when I load the > new model. > > Thanks in advance! > > kc > Try out our automatic atom reconnection tool (by myself and Tom Transue) here: http://spdbv.niehs.nih.gov/resources/ (note: The dials stuff there needs updating) It uses a perl script encapsulated in an O text database object. It has a list of covalent radii to detect bonds between all atoms. It is not advanced enough to deal with alternate conformations, but it does a good job otherwise. Oh, it also assumes that O's ATOM_Z property is correct. Since RCSB has dropped the element-aligned atom naming rule, many elements are mis-detected for ligands in newer PDB files. Maybe Alwyn can implement the new element column. (Or maybe it's in the latest version which I'm not using yet?) Also: I noticed that the listinfo/o-info like that comes with this list email has links for Alwyn's O pages that are out of date. Joe _______________________________________________ o-info mailing list (moderated) o-info@o-info.bioxray.dk http://o-info.bioxray.dk/mailman/listinfo/o-info
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