[PyMOL] General script

[Mark Zierden]

Hi,

In the PyMolWiki under simple scripting parts of the command lines are
color coded(red, blue and green). What does that mean?

cmd.extend(“doSimpleThing”,doSimpleThing)
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Re: [PyMOL] PyMOL-users Digest, Vol 114, Issue 7

[Honegger Annemarie]

I like the way the Protein-Ligand Interaction Profiler (PLIP,  
https://projects.biotec.tu-dresden.de/plip-web/plip/index , 
https://pypi.python.org/pypi/plip , 
http://nar.oxfordjournals.org/content/early/2015/04/14/nar.gkv315.full ) 
highlights different interactions in its PyMol output file, such as Pi-Pi 
stacking, Pi-cation interactions, salt bridges etc. The algorithms and cut-offs 
used are detailed on the Help page of the server site. It would be nice to be 
able to apply similar analyses directly in PyMOL, not only to 
Protein-Ligand(HETATM)  interactions, but also to protein-protein interactions.

best regards

Annemarie

> 
> What I've done before is to draw a line between two pseudo-atoms placed 
> at the center of each ring.
> 
> HTH,
> Matthew Baumgartner
> 
> On 11/10/2015 02:08 AM, Albert wrote:
>> I think the major concern is how Pymol depicts the pi-pi stacking 
>> Of course we can identify such interaction immediately as soon as we 
>> open the system in Pymol.
>> 
>> However there is no any  components to indicate this, eg: we can 
>> depict the H-bond with a dash between two atoms but how could pi-pi 
>> interaction be depicted?
>> 
>> 
>> 
>> On 11/10/2015 07:03 AM, Osvaldo Martin wrote:
>>> Hi Amali,
>>> 
>>> I am not aware that PyMOL has this feature implemented 
>>> out-of-the-box. Nevertheless this can be done with PyMOL. A crude 
>>> approximation will be to measure the distance between the center of 
>>> aromatic rings and consider a pi-pi stacking for distances shorter 
>>> than a threshold value. A better model will probably include a 
>>> distance threshold and one or two angles in the definition.
>>> 
>>> Are you trying to estimate pi-pi stacking interactions in general or 
>>> for a particular system?
>>> 
>>> Cheers,
>>> Osvaldo.
>> 


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Re: [PyMOL] H bonds

[Matthew Baumgartner]

Hi Amali,

For adding hydrogens, I have found that PyMOL does an OK job normally, 
but if you need more accurate placement of hydrogens, I can recommend 
using Reduce.


http://kinemage.biochem.duke.edu/software/reduce.php

HTH,
Matthew Baumgartner


On 11/11/2015 02:06 AM, Osvaldo Martin wrote:

Hi Amali,

Aspartic acid is also assumed to be charged (like Arg), but with 
opposite sign. Acids like Asp release hydrogens, bases like Arg accept 
hydrogens. That's why in one case there is one hydrogen more that what 
you are expecting and in the other case there is one hydrogen less. 
Nothing wrong with PyMOL, is just assuming the most plausible scenario 
(at pH 7) anyone can assume without any other information and without 
solving equations like the Poisson-Boltzmann equation. Almost every 
molecular modeling package out there is making the same assumptions.


Cheers,
Osvaldo.





On Wed, Nov 11, 2015 at 7:50 AM, Amali Guruge > wrote:


Dear Prof. Osvaldo,

Arg residue problem is solved. Thank you very much. Other thing is
for Aspartic acid the program doesn't add H to the OH
group. What is the reason behind this.

Thank you.

On Wed, Nov 11, 2015 at 11:17 AM, Osvaldo Martin
> wrote:

Hi Amali,

By the =NH group do you mean one of the nitrogens of the
guanidine group? If that's the case PyMOL is doing the right
thing. By default PyMOL assumes that (Arg, Lys, Glu, Asp) are
charged. In general that's a reasonable assumption (if
residues are exposed to the solvent or relative close to other
charges of the opposite sign), Is not a good assumption if you
have Arg too close to others Arg, Lys or other residue of
equal sign.

What is the other think you notice?

Cheers,
Osvaldo.
PD: please just call me Osvaldo.


On Wed, Nov 11, 2015 at 6:25 AM, Amali Guruge
> wrote:

Dear Prof. Osvaldo,

When I use the command h_add, the pymol program adds H to
the enzyme. But when it contains Arg group it added two
hydrogens to =NH group. How can I solve that problem? I
noticed another thing.

Thank you in advance.

On Mon, Nov 9, 2015 at 6:00 PM, Amali Guruge
> wrote:

Thank you very much for the reply.

On Sat, Nov 7, 2015 at 1:34 PM, Osvaldo Martin
>
wrote:

Hi Amali,

PyMOL has parameters like h_bond_max_angle that
are defined in terms of aceptor-donor-hydrogen,
hence if hydrogens are not present PyMOL has to
guess the position of hydrogens.

If you need to add hydrogens you can use PyMOL’s
h_add 
command, alternatively you can use openbabel
.

Cheers,

Osvaldo.

On Sat, Nov 7, 2015 at 2:33 AM, Amali Guruge
> wrote:

Dear All,

My question is related to find the polar
contacts between an enzyme and ligand. I want
to know  when we find polar contacts,

1) protein should contain H atoms or not?

2) ligand molecule should contain all H atoms
or not

Please can anyone help me.

Thank you in advance.


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