pymol-users

[PyMOL] add polar/aromatic hydrogen

[lina <lin...@gm...>]

Hi,

How to add polar/aromaic hydrogen's quickly?

in A-->hydrogen -- only add all hydrogen,

thanks for any suggestions,


-- 
Best Regards,

lina

Re: [PyMOL] add polar/aromatic hydrogen

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

Hi lina,

to add polar hydrogens, try this:

h_add acceptors or donors

I don't know if it's possible to select aromatic atoms in PyMOL.

Cheers,
   Thomas

On 09/06/2011 09:12 AM, lina wrote:
> Hi,
>
> How to add polar/aromaic hydrogen's quickly?
>
> in A-->hydrogen -- only add all hydrogen,
>
> thanks for any suggestions,


-- 
Thomas Holder
MPI for Developmental Biology

Re: [PyMOL] add polar/aromatic hydrogen

[lina <lin...@gm...>]

On Tue, Sep 6, 2011 at 4:27 PM, Thomas Holder
<sp...@us...> wrote:
> Hi lina,
>
> to add polar hydrogens, try this:
>
> h_add acceptors or donors

Thanks,

in my situation, is it possible to add hydrogens (polar) one in whole protein,
not consider acceptors or donors,

>
> I don't know if it's possible to select aromatic atoms in PyMOL.
>
> Cheers,
>  Thomas
>
> On 09/06/2011 09:12 AM, lina wrote:
>>
>> Hi,
>>
>> How to add polar/aromaic hydrogen's quickly?
>>
>> in A-->hydrogen -- only add all hydrogen,
>>
>> thanks for any suggestions,
>
>
> --
> Thomas Holder
> MPI for Developmental Biology
>



-- 
Best Regards,

lina

Re: [PyMOL] add polar/aromatic hydrogen

[lina <lin...@gm...>]

On Tue, Sep 6, 2011 at 4:27 PM, Thomas Holder
<sp...@us...> wrote:
> Hi lina,
>
> to add polar hydrogens, try this:
>
> h_add acceptors or donors

Thanks.

it works for selections,

what if when I use h_add selections
I only want to add one H, not two H

How can I achieve this.

Thanks again.
>
> I don't know if it's possible to select aromatic atoms in PyMOL.
>
> Cheers,
>  Thomas
>
> On 09/06/2011 09:12 AM, lina wrote:
>>
>> Hi,
>>
>> How to add polar/aromaic hydrogen's quickly?
>>
>> in A-->hydrogen -- only add all hydrogen,
>>
>> thanks for any suggestions,
>
>
> --
> Thomas Holder
> MPI for Developmental Biology
>



-- 
Best Regards,

lina

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

Re: [PyMOL] add polar/aromatic hydrogen

[lina <lin...@gm...>]

On Wed, Sep 7, 2011 at 12:02 AM, Thomas Holder
<sp...@us...> wrote:
> 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,

I will try.

Thanks again for your help.

>
> Cheers,
>  Thomas
>
> --
> Thomas Holder
> MPI for Developmental Biology
>



-- 
Best Regards,

lina