>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. the stereo_chem.odb entry contains the residue connectivity used by O to generate the 'bonds' you see on the screen. if your molecule does not have a descriptor in this entry, O tries to connect within just the residue using a set of distance criteria. so you have a few choices: 1/ do nothing. the 'bonds' on the screen don't mean a lot about your stereochemistry so you do NOT have to have them all. O uses the screen connectivity for some commands (eg. tor_gen, graqb_group) otherwise they are cosmetic. 2/ make a new entry in the stereo_chem.odb for you residue. this is 'easy'. the entry does not have to be full, i.e. describing all the stereochemistry etc, just the connect records and usually just the 'connect_all' records are sufficient. if you want to rebuild the residue, you might want to add a few more things. remember to change the line count at the header record for the ODB entry. drop me a line if you need help 3/ make a little macro to draw each extra bond that you'll need to activate every time you read in new coords. something like this for each bond: bond_make term_id m1 a5 O obj term_id m1 a6 N obj .... happy valentine's day Alwyn Jones alwyn@xray.bmc.uu.se http://xray.bmc.uu.se/alwyn _______________________________________________ o-info mailing list (moderated) o-info@o-info.bioxray.dk http://o-info.bioxray.dk/mailman/listinfo/o-info
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