João,
Thanks for being patient on this. I just moved to a big city and am
still getting settled.
PyMOL does indeed need four passes. It fills in hydrogens one at a
time, positioning them in idealized locations based upon the structure
of the neighbor to which it will be bound. If it's adding h
Hey Jason!
Thanks for the reply, no problem at all with the delay :)
I got my hands around the code and I *think* I got it to add hydrogens to a
protein (including checking that random effect).
My only question is, how PyMol determines which atoms lack hydrogens. I
checked the hetatm.py and prot
Ooops, got overzealous with button pushing and that email went out
before I was ready. Continuing...
Another point: if the position of the hydrogen to add is ambiguous,
PyMOL will randomly choose a position. (You can see this by creating
a methane group from the builder, removing all hydrogens,
João,
The function you're looking for is:
void ObjectMoleculeAddSeleHydrogens(ObjectMolecule * I, int sele, int state)
in layer2/ObjectMolecule.c line 3629 (or thereabouts). PyMOL has a
connectivity table that determines which atoms are bound to which
others. Read over that function and se
Hey Jason,
Thanks! I'd "traced" add_H to that function before but my knowledge of C is
rudimentary so I was quite overwhelmed.
Yet, I think I managed to understand a bit better what's going on, but
correct me if I'm wrong. It seems PyMol looks for neighbours first, derives
a "bonding network" fro
Hi,
Okay, maybe I should delve into the code for this, but I (and probably
Joao too) was wondering how (if) Pymol determines the valence of a
bond. I.e. can Pymol distinguish between ethane, ethene, and ethyne?
Cheers,
Tsjerk
On Thu, Jul 1, 2010 at 5:58 PM, João Rodrigues wrote:
> Hey Jason,
>
