I've been using Molmol, but found significant issues when working with a non-standard structure. For example - I have a cyclic peptide with ornithine residue creating the cycle.
Molmol won't open PDB's with ornithine unless a residue definition is provided. I've never given any thought on how that can be done. Molmol does, however open XYZ files, albeit with a loss of residue information, which makes it very difficult to perform selections.
Are there any good alternatives to MOLMOL for working with structure bundles? Can pymol or anything else visualize bundles of custom molecules? (i.e. not built of standard protein/nucleic acid residues)
edit: found out that pymol does display bundles of molecules, but the individual molecules must be originally oriented the same way in the source pdb files (otherwise bundle looks completely disordered). That can be done, for example with by running
Perhpas VMD-Xplor does what you want? I'm not sure as I have not used it much myself, but I believe this software is orientated towards NMR users.
answered Mar 01 '10 at 11:53
You can try pymol or chimera. I've used them to show metal bound cys residues.
answered Mar 02 '10 at 06:18