Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

[James S. <jms...@gm...>]

Hi Christian!

As I understood that LigPlot is not free for accademical ussage isnt?

By the way in that paper
http://onlinelibrary.wiley.com.sci-hub.org/doi/10.1002/minf.201000167/pdf
there is exhaustive comparison of three different packages for such 2D
diagram generation. Have anybody used such software else ?


James

2012/6/26 Christian Roth <chr...@bb...>

> Hi James,
>
> the program you can use for this is ligplot from Roman Laskowski at the
> EBI.
> the solvent accessability shading is done with the help of naccess.
>
>
> Best Regards
>
> Christian
> Am Dienstag 26 Juni 2012 08:07:07 schrieben Sie:
> > By the way
> >
> > in some papers I've seen  2D schematic diagrams of the protein-ligand
> > interactions.
> > The exapmle of such maps could be found here
> >
> http://ars.els-cdn.com.sci-hub.org/content/image/1-s2.0-S0005273610001707-g
> > r4.jpg
> >
> >  Could you tell me examples of software wich could produce such maps?
> >
> >
> > Thanks
> >
> > James
> >
> > 2012/6/15 James Starlight <jms...@gm...>
> >
> > > Thomas, thanks this works perfect.
> > >
> > >
> > > Jason,  I've tested  this script on my system ( this is the membrane
> > > protein inserted in the bilayer surrounded by two water layers ( up and
> > > down ). During simulation individual water mollecules move into the
> > > protein interiour ( in that case protein like a water pore althought
> it's
> > > the receptor ) so I want to visualise only that buried water.
> > >
> > > I've tried to do it via find_buried_waters script both via ASA as well
> as
> > > in case when I've used small cutoffs ( 0.1) but the script selected too
> > > many waters ( e.g virtually all waters from up and down layers have
> been
> > > selected ). How I could specify this selection more carefully ?
> > >
> > > find_buried_waters 1, 0.1
> > >
> > >
> > > James
> > >
> > >
> > > 2012/6/12 Thomas Holder <sp...@us...>
> > >
> > >> This will show them in the same slot in group mode.
> > >>
> > >>
> > >> sorry, not "group mode" but "grid mode" of course.
> > >>
> > >>
> > >> --
> > >> Thomas Holder
> > >> MPI for Developmental Biology
> > >> Spemannstr. 35
> > >> D-72076 Tübingen
> >
>
>
>