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

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

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, and then
h_adding them back.  Remove/add them a few times to the lone carbon to
see the effect of the randomized placement.)

Cheers,

-- Jason



On Thu, Jul 1, 2010 at 10:40 AM, Jason Vertrees
<jas...@sc...> wrote:
> 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
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120