Re: [PyMOL] add polar/aromatic hydrogen

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

Hi Lina,

> Hope you won't mind this email sent to you directly.

not at all, that made it finally clear what you actually want!

> Here I attached the pdb,
>
> which I want to add the aromatic H,
>
> The cur_1.pdb:  only polar H was added.
>
> while cur_11.pdb I used h_add (selection of aromatic atom, namely C3,
> C5, C6, C16, C17, C20)
>
> I only kept one H here, and removed another.

PyMOL only knows bond valences for known amino acids, but your file 
contains a molecule which is not a protein. You can either explicitly 
define which bonds are aromatic or double bonds, or PyMOL can guess for 
you from geometry.


# load molecule without hydrogens
load cur_1.pdb
remove hydro

# show double-bonds in line or stick representation
set valence

# make rings aromatic and C=O double bonds
valence guess, all, all

# add hydrogens
h_add all


If it does not work to guess valences, you need explicit statements:


# select rings
select ring1, name C2+C3+C4+C5+C6+C7
select ring2, name C15+C16+C17+C18+C19+C20

# make rings aromatic
valence aromatic, ring1, ring1
valence aromatic, ring2, ring2

# define double bonds
valence 2, name C10, name O3
valence 2, name C12, name O4


Hope that helps,

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology