Re: [PyMOL] How does PyMol add hydrogen atoms?

[Jason V. <jas...@sc...>]

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 hydrogens
to a planar, linear or tetrahedral arrangement, PyMOL places the atoms
in different -- idealized -- locations.  PyMOL finds the open valence
vector for and fills positions according to that.

On Tue, Jun 22, 2010 at 3:42 PM, João Rodrigues <an...@gm...> wrote:
> Hello all,
>
> I've been looking at Pymol's code for sometime time now and yet the
> algorithm for addition of hydrogen atoms to molecules in Pymol is not clear
> to me..
>
> I've traced the h_add function to OMOP_AddHydrogens in layer2/Executive.c:
>
>     op.code = OMOP_AddHydrogens;        /* 4 passes completes the job */
>
> I'd argue this "4 passes to complete the job" requirement is related with
> the algorithm in chempy/place.py that iterates over a "need" list of lists.
>
>             need = [ [], [], [], [] ]
>
> This list of lists hold info for heavy atoms that lack 1, 2, 3, or 4 atoms.
>
> This seems quite logical. But then the H atoms added have names like H01,
> H02, etc, when they were correctly identified in chempy/proteins.py and have
> their names in protein_amber.py and protein_residues.py.
>
> My main questions are: are there different treatments for proteins when it
> comes to H-addition? How are H-s added to say, Methane? (given a single C).
>
> Best!
>
> João [...] Rodrigues
> @ http://doeidoei.wordpress.org
>
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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