[PyMOL] A little script for massaging pdb files

The electron densities of Carbon, Nitrogen and Oxygen look basically the
same to crystallographers.  So, sometimes they get them confused in
pdb files.  In particular, one often has to flip the orientation of the
side chains in Asn or Gln.  Also, this means that the Nitrogens may be
placed incorrectly in His side chains.  Similarly, since x-ray
crystallographers cannot see Hydrogens, the crystal structure may not tell
you which Nitrogen(s) in the His residue should be protonated.  If you're
going to use the crystal structure in, for example, a molecular dynamics
calculation, it is critical that you get this stuff right.  The easiest
way to do this is to try out each possibility and see which one looks best
with respect to Hydrogen bonding.  Since PyMOL is so easy to script, I
wrote a little bit of code to automate this process.  You can find the
code at

http://www.umich.edu/~mlerner/mgzoom.py

and a little bit of explaination at

http://www.umich.edu/~mlerner/pymolscripts.html

It basically lets you scan through the Asn, Gln and His residues and pick
the proper orientation/protonation.  If I can figure out how, maybe I'll
turn it into a wizard.

I had a quick question that I came across when writing this script:

I was looking for some way to set a bond valence, and all I could find was
cycle_valence.  Is there something like set_valence?  My guess is that it
would look something like this:

/*========================================================================*/
void EditorSetValence(int valence)
{
  CEditor *I = &Editor;
  int sele0,sele1;

  if(I->Obj) {

    ObjectMoleculeVerifyChemistry(I->Obj); /* remember chemistry for later */

    sele0 = SelectorIndexByName(cEditorSele1);
    if(sele0>=0) {
      sele1 = SelectorIndexByName(cEditorSele2);
      if(sele1>=0) {
        /* bond mode */
        /* should we care if valence > 3? */
        ObjectMoleculeAdjustBonds(I->Obj,sele0,sele1,0,valence);
      }
    }
  }

}

But I didn't see it in layer3/Editor.c.  Is it somewhere else and I just
haven't found it?

Thanks,

-michael

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