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 ?
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.
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
> The exapmle of such maps could be found here
> Could you tell me examples of software wich could produce such maps?
> 2012/6/15 James Starlight <firstname.lastname@example.org>
> > 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 <email@example.com>
> >> 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