On Tuesday, April 8, 2003, at 09:51 AM, Geoffrey H Wathen wrote:
Currently, I'm exploring using Chimera to visualize chemical interactions. I know that this can be done using multiple pdb files, and the 'Save Session' command. (Indeed, this might be a better way to have Chimera handle it, as it seems that Chimera doesn't like finding hydrogen bonds between models in a single PDB file.) The one thing that is lacking in this approach is the ability to talk to other applications that can read PDB files, but, clearly, not the Chimera PY session files.
Hi Geoff, I guess I'll enable 'write PDB' for multiple models and offer the option of writing to a single file or to multiple files distinguished by model number. FindHBond doesn't offer to find cross-sub-model hydrogen bonds since the only standard PDB files that have multiple models are ones containing different conformers of the same structure -- rather than heterogeneous models. I could allow cross-sub-model hydrogen bonds if you felt there was a real need even after the 'write PDB' change above.
As to the 'backdoor' method I'm using to add atoms, it's nothing so glamorous as programming in Python. Indeed, it's simply manually writing in the atom's code into the PDB file. By making it a separate model (using the END command), I can manipulate it separately from the rest of the PDB file, move it into the proper location, then write the PDB file out again. I can then edit the PDB file to remove the END command, and the atom is part of the overall structure. I am also working on a better way to do this by writing a program that will allow me to work within a better dimensional framework for placing the new atom, then will write out a PDB file. We'll see how it goes...
Never underestimate the ingenuity of frustrated users. :-) Obviously, the structure editing I'll be adding will be somewhat easier than this to use, but it's still a couple of releases down the line -- so keep using what works! I am impressed. :-) Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu