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 
mailto: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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[PyMOL] pymol alignment help

[Clarisa Alvarez]

Hello!
could someone help me to download a pymol alignment? and know with which
score it makes the alignment.
Thanks in advance.

Clarisa.
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