Dear all :)
I want to find Hbonds beetween different helices in the membrane receptor (
H bonds beetween sidechains only)
I know possible way to do it wihin selection if I defined different helixes
but is there any way to find almost all Hbonds between polar sidecains
groups ?
Could I use
Thanks, Thomas, Jason
both of the methods are useable :)
By the way I've forced with the problem of the representation of the active
sites of different enzymes. I need to view all my protein as the cartoons
and the ligand as the shpere in the ligand binding pocket. Besides I need
to mark
James,
Is there any semi-avtomated way to find ligand binding pocket and do all
such things ?
For your given object, click A preset ligands sites cartoon. Try
other options under that menu.
Cheers,
-- Jason
2011/11/28 Thomas Holder spel...@users.sourceforge.net
Hi James,
most
Thanks Jason.
It works quite well in case of not very compliated ligands ( e.g bonds
beetween aa-tRNA and the aa-tRNA syntase were correct ) but in the
sugar-bound enzyme there were some mistakes in representation of the
H-bonds netween water/ligand/active center ( some water also partisipate in
Another question also linked with the non-covalent interaction.
In particular I wounder to know how i Could represent all hydrophobic ( Ley
Ile Val etc) sidechains in my proteins in most trivial manner? I'd like to
represent the hydrophobic core of the proteins made from those residues.
Thanks,
Hi James,
most trivial manner:
as cartoon
show sticks, resn LEU+ILE+VAL
set cartoon_side_chain_helper
and eventually something like this:
show spheres, resn LEU+ILE+VAL and not name N+O+C
set sphere_transparency, 0.5
Cheers,
Thomas
On 11/28/2011 02:58 PM, James Starlight wrote:
Another
Hi James,
As I've understood there are no posible ways to represent H-bonds in
proteins in explicit manner. So I'm looking for possible way to do it
via some plugin or another way.
PyMOL can find polar contacts and represent them as dashed lines. You
don't need any extra plugin.
Thomas, thank you for so detailed explanation.
This way works good but I'd like to ask you about possibe Hbonds in the
protein chain.
As I remember for protein physics courses the H atom is always donor for
only ONE H-bond ( and O or N atoms could be akceptors for 1 or 2 Hbonds)
But In my case
While the single acceptor H-bond is most common, bifurcated (or three-centred)
H-bods are
not uncommon in crystal structures, as described starting page 22 of GA
Jeffrey's book:
Dear PyMol users!
As I've understood there are no posible ways to represent H-bonds in
proteins in explicit manner. So I'm looking for possible way to do it via
some plugin or another way.
In particular I need
1) to visualize H-bonds in some structural motifs like coiled coil wich are
dimers
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