Getting Started
-Structure Dataset
-DNA rendering
-Surface Dataset
-Scalar Field Dataset: X-ray
-Scalar Field Dataset: EM
-Topograph Dataset
-Electrostatic Potential I
-Electrostatic Potential II
-Geometric Primitives
-Stereo output
-Saving the viewing matrix


Surface Dataset

A short introduction into displaying molecular surfaces.

Following the DINO philosophie, a molecular surface is not created by the program, but is generated externally with e.g. MSMS or MSP.

With MSMS, the PDB file is first converted into an .xyzr file, which contains the coordinates and the radius of each atom. (This is done with pdb_to_xyzr from the MSMS distro or with pdb2xyzr , a perl script which carries the definition file within and is slightly faster). This .xyzr file is then used as input for MSMS and the result are two files: a .vert and a .face file.

> pdb2xyzr NAME.pdb > NAME.xyzr
> msms -if NAME.xyzr -of NAME
> ls
NAME.pdb  NAME.xyzr  NAME.face  NAME.vert

Download this tutorial: surf.tar.gz
// load the structure dataset
load iib.pdb -name iib

// load the surface dataset
load iib -type msms -name surf

// attach the surface to the structure
// (thereby assigning each surface point
// to an atom)
.surf attach .iib

// center on the surface
scene center [.surf]

// create a surface object 
.surf new -name all

// adjust the clipping planes
scene autoslab

// color the surface object according
// to some underlying residue properties
// the variables used here are predefined
// by DINO, use 'var' to look at them
.surf.all set color=blue -sel $basic
.surf.all set color=blue4 -sel $basic2
.surf.all set color=red -sel $acidic
.surf.all set color=red4 -sel $acidic2
.surf.all set color=cyan -sel $polar
.surf.all set color=green -sel $aromatic
.surf.all set color=yellow -sel $aliphatic

// reset the color to white and make the surface
// transparent  to show the underlying structure
.surf.all set color=white
.iib new -name all
.iib.all render custom
.surf.all render t=0.4

// generate a solid surface
// reset transparency and hide struct obj
.surf.all render t=1
.iib.all hide

scene set near+=23
.surf.all render solid,solidc=grey