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 -- This isn't a democracy;| _ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
