Re: [PyMOL] Active site in Pymol

[Julian Heinrich]

Hi,

you can use the Measurement Wizard to get distances between atoms. PyMOL
will also print the residue type in the console if you click on any atom.

Best,
Julian


On Tue, Aug 23, 2016 at 8:45 AM Farzaneh Namazifar <
f.namazifar706...@gmail.com> wrote:

> Hi Dear all;
> I am a PyMol user.  I read the PyMOL tutorial
> 
>  about
> the hydrogen bond. I need some informations about hydrogen bond like:
> 1- length of hydrogen bond between two residue
> 2- which kind of residues are in the hydrogen bond
> 3- Number of hydrogen bond in active site
> As above, I need informations about  Hydrophobicity of residues in the
> active site. and else information about pi-pi interaction in DNA... I need
> your help ...
> Best Regards.
> Thank you in advance.
>
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Re: [PyMOL] Active site in Pymol

[Sampson, Jared M.]

Hi Farzaneh -

Are you looking for something programmatic to use for many different 
structures, or just analyzing a single structure?

With just one structure (or a few) you can do most of this using the GUI by eye.

1. To find the length of each H-bond involving your ligand, (let's say the 
object or selection is called "my_ligand"), click "S (show) > Labels" for the 
'my_ligand_polar_conts' object that was created when finding the H-bonds.

2. To see which kinds of residues are involved, you can type on the PyMOL 
command line: `show sticks, byres (my_ligand within 4)` which will show sticks 
for the entire residue (byres) of any residue with any atom within 4 Å of 
my_ligand.

3. For the number of H-bonds in an individual active site, you can probably 
just count them by eye.

Alternatively, if you need a more automated approach, have a look at Thomas 
Holder's Polarpairs plugin: http://www.pymolwiki.org/index.php/Polarpairs

Hope that helps.

Cheers,
Jared



On Aug 23, 2016, at 2:39 AM, Farzaneh Namazifar 
> wrote:

Hi Dear all;
I am a PyMol user.  I read the PyMOL 
tutorial
 about the hydrogen bond. I need some informations about hydrogen bond like:
1- length of hydrogen bond between two residue
2- which kind of residues are in the hydrogen bond
3- Number of hydrogen bond in active site
As above, I need informations about  Hydrophobicity of residues in the active 
site. and else information about pi-pi interaction in DNA... I need your help 
...
Best Regards.
Thank you in advance.
--
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(PyMOL-users@lists.sourceforge.net)
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[PyMOL] Active site in Pymol

[Farzaneh Namazifar]

Hi Dear all;
I am a PyMol user.  I read the PyMOL tutorial

about
the hydrogen bond. I need some informations about hydrogen bond like:
1- length of hydrogen bond between two residue
2- which kind of residues are in the hydrogen bond
3- Number of hydrogen bond in active site
As above, I need informations about  Hydrophobicity of residues in the
active site. and else information about pi-pi interaction in DNA... I need
your help ...
Best Regards.
Thank you in advance.
--
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Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net