Now to a comment. After some tinkering, I finally managed to output a new PDB file that contained models from several other PDB files. This, however, wasn't exactly an easy of intuitive thing to do. My first thought had been to use the 'Write PDB' command in the Model Panel. However, that button automatically greys itself out when more than one model is selected. I finally stumbled upon the command line command 'pdbrun cat > file'. So, I was able to do what I wanted, but I had to go through a rather backdoor method. Any chance that things like 'Write PDB' will be enabled when more than one model is selected?
I could enable 'write PDB' with multiple models selected. I guess my question is why do you want multiple PDB models in a single file? What will you do with that file? Knowing how you want to use the file will help me decide if simply enabling the button is the way to go or if some other interface is more appropriate. If I enabled it, the models would be separated by END records.
And what about a method of adding more atoms, other than just hydrogen? (I also know of 'backdoor' ways that I can do this, but I'd love to see Chimera become a more fully featured molecular modeler, and to that end, I'm quite happy to give all kinds of input.)
I'm currently working on smarter hydrogen addition (avoiding steric conflicts and maintaining hydrogen-bonding interactions). I should be done with that in time for our next release. I intend to work on some limited structure-building features after that. So a preliminary version might be available two releases from now. Even I'm not aware of backdoor ways to add non-hydrogen atoms! I guess the swapaa command _sort_ of does this, but it's not at all generic. Are you writing Python code to do this? Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu