pymol-users

[PyMOL] Help

[Babban M. <bab...@gm...>]

Dear users,

Is there some program to calculate the zeta potential or streaming
potential
of protein molecules (PDB files )

Is there some program to calculate the dipole moment of protein molecules
at
different PH values?


My last doubt is about creating polymers out a given PDB ?
I am studying the fibrils of some proteins and although the structure of
fibril is not know but through some analysis I have come to understand the
region in peptide which is leading to fibrillation.

I want to be able to create a PDB which has like 4/8/16 monomeric peptide
combined through some BETA PLEATED region(i.e the peptides will
join/aggregate around that region (beta region) of the peptide ) and all I
have is the PDB of the monomeric peptide.

Is there a possibility to make such peptides in Pymol or something ? Please
advise.


Thanks for your help.

Sincerely

[PyMOL] Help

[Vertika G. <var...@gm...>]

Hi!

I am new user.
>From a 3DRISM analysis
1. I want to show iso-surface of a potential map (.dx) and another
2. explicit distribution (.pdb) which should be colored by index from low
to high,(e.g. red to blue).


 Thanks in advance!
-- 
Vertika Gautam

Research Assistant
Drug Design and Development Research Group (DDDRG)
Department of Chemistry, Faculty of Science
University of Malaya



*e-mail address: var...@gm...
<var...@gm...>
var...@ho... <var...@ho...>
    01112294191*

Re: [PyMOL] Help

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

Hi Babban,

regarding your questions on peptide building:

> My last doubt is about creating polymers out a given PDB ?
> I am studying the fibrils of some proteins and although the structure of 
> fibril is not know but through some analysis I have come to understand 
> the region in peptide which is leading to fibrillation.

PyMOL has a builder where you can create a peptide with given secondary 
structure. In the external GUI click on "Builder" on the right and then 
"Protein" on the left side.

You may also check this PyMOLWiki page:
http://www.pymolwiki.org/index.php/Peptide_Sequence

> I want to be able to create a PDB which has like 4/8/16 monomeric 
> peptide combined through some BETA PLEATED region(i.e the peptides will 
> join/aggregate around that region (beta region) of the peptide ) and all 
> I have is the PDB of the monomeric peptide.

As far as I know there's no build-in PyMOL function that sticks together 
two beta-strands.

In editing mode you can freely drag around objects: Right-click, "drag 
object coords", SHIFT+Middle-Mouse-Drag.

More precide movements can be achived with translate and rotate commands:
http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures#Translate_or_rotate_individual_objects

If this is not precise enough for you and you want real beta-sheet 
modeling, you should use something like modeller.

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Re: [PyMOL] Help

[Tsjerk W. <ts...@gm...>]

Hi Babban,

For modeling the polymers you probably want to try a docking program.
Maybe HADDOCK suits your needs...

Hope it helps,

Tsjerk

On Sun, Jul 31, 2011 at 1:42 AM, Babban Mia <bab...@gm...> wrote:
> Dear users,
>
> Is there some program to calculate the zeta potential or streaming
> potential
> of protein molecules (PDB files )
>
> Is there some program to calculate the dipole moment of protein molecules
> at
> different PH values?
>
>
> My last doubt is about creating polymers out a given PDB ?
> I am studying the fibrils of some proteins and although the structure of
> fibril is not know but through some analysis I have come to understand the
> region in peptide which is leading to fibrillation.
> I want to be able to create a PDB which has like 4/8/16 monomeric peptide
> combined through some BETA PLEATED region(i.e the peptides will
> join/aggregate around that region (beta region) of the peptide ) and all I
> have is the PDB of the monomeric peptide.
> Is there a possibility to make such peptides in Pymol or something ? Please
> advise.
>
> Thanks for your help.
>
> Sincerely
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands