I'm having a bit of a torrid time trying to get Modeller4 to cope with hydrogens. Here's the scenario: I have a template pdb file (directly from the Brookhaven PDB databank) which contains an NMR structure and therefore contains all hydrogens. Looking at the FAQ in Modeller's documentation I find that I probably need to add the following lines to get-model.top: SET HYDROGEN_IO=on SET TOPOLOGY_MODEL=1 SET TOPLIB = '${LIB}/top.lib' SET PARLIB = '${LIB}/par.lib' I then run Modeller in the usual way and end up with models with a huge number of violations, and whopping great big gaps in the backbone. Strangely, if I strip the pdb file of all its hydrogens, remove the SET HYDROGEN_IO=on and put TOPOLOGY_MODEL to 3 everything is fine - a nice model is made, but, of course, without any hydrogens. I'm probably doing something daft - can anyone out there point me in the direction? Many thanks. Brian. --------------------------------------------------------------------- Brian Marsden marsden@bioch.ox.ac.uk Home: +44 1865 552696 OCMS, Oxford Fax: +44 1865 275253 Work: +44 1865 275720 ---------------------------------------------------------------------