On 7/12/10 3:31 PM, Dave Barkan wrote: > I was wondering if there is a quick way to set up force field restraints > on a hierarchy of atoms generated by read_pdb()? Right now I have to > explicitly set up three or four types of restraints myself (following > the protocol in the charm_forcefield.py example in the atom module). > This is likely to be re-implemented often and it would be nice if IMP > provided an easy way to do this.
Indeed - this is a common task. I have such a simplified wrapper available but haven't added it yet. Note that there are several steps because "adding a forcefield" isn't just a case of adding a restraint, but also requires topology, etc. to be set up properly.
> Maybe less useful to others, but potentially to me, would be if you > could specify a region of the protein to which to add the forcefield > restraints (instead of the whole PDB you just read in).
You can create topology for any Hierarchy - doesn't have to be the entire PDB, but could be a single chain, for example.
Ben