>Can anybody tell me how to get a helix segment with one aa methylated? o's treatment of non-standard groups is simple. it doesn't care about them if all you want to do is look at them. if, on the other hand, you want to make them from scratch, or rebuild them, it is either a bit of a pain in the kneck, or requires some work. to be a proper member of os standard residue types, you need 1. a connectivity entry (also used by the mutate commands to add the right atoms into your molecule) 2. a torsion entry if you want to use tor_residue. you can use tor_general (where you id the atoms) on any old thing 3. an entry to explain how to split up the residue for move_frag & rsr_zone 4. an entry in the refi_zone dictionary 5. lego_side entry (needs to be an amino-acid or a close relative, at present). if you want a quickanddirty fix, i would add the atoms to the input pdb file (placing them 1 angstreom away from bonded mates), and then just grab_atom to where you want them to be. if you plan to refine your structure in xplor... you will need a dictionary. then just place the atoms close enough to where you want them in o (with roughly correct geometry) so that your refinement program does not break. if you have coords for a new ligand (from a small molecule database), load them into o, grab_group them to where you want them, tor_general bits of them to keep stereochemistry. alwyn (web home page http://alpha2.bmc.uu.se/~alwyn )
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