Re: [PyMOL] Addition of the missing hydrogen atoms

[Thomas H. <sp...@us...>]

Hi James,

the selection makes the flexibility:

# Example: non-polar residue carbons
remove hydro
h_add (resn ILE+LEU+VAL+MET) and (elem C)

# Example: polar but not backbone
remove hydro
h_add (acceptors or donors) and not (name N+O)

Also bond order and formal_charge determine where to add a hydrogen.

Cheers,
   Thomas

On 01/23/2012 02:50 PM, James Starlight wrote:
> Dear PyMol users!
>
> I have one extra question about addition of the missing Hydrogen atoms
> to my structure.
>
> I've found that I could do it via context Hydrogen command as well as
> via H_add command.
>
> Now I want to add only specific hydrogens to the specific residues of my
> proteins ( e.g only alymphatic hydrogens to the non polar residues etc)
>
> Might It be done in PyMOL?
>
> Here http://www.pymolwiki.org/index.php/H_Add I've found only very chort
> description of the H_add command but I know that this one has some
> flexibility.
>
> Thanks,
>
> James

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen