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



This is from the PDB file 1MNM (yeast matalpha2/mcm1/dna ternary transcription complex, S. Tan, T.J. Richmond, Nature 391 1998).

I did a quick search through the database to find similar sequences to MCM1 (containing the MADS box), aligned them and analyzed the result with Alscript (G.J. Barton, Protein Engineering 6). I used the similarity codes 4,6,8 and 10 to select residues in the structure with increasing conservation among the sequences.

Download this tutorial: mads.tar.gz
// from 1MNM (Tan et. al. (1998) Nature 391)

// set variables
set c10 (rnum=18,26,35,38,39,42,45,46,47,49,50)
set c8  (rnum=20,23,32,36,40,43,54,58,60,61,72)
set c6  (rnum=21,28,31,34,37,44,51,52,56,62,64,67,69)
set c4  (rnum=25,55,57,59,63,70,71)

// load datasets
load mads.pdb
load mads_p1 -type msms -name smcm1
load mads_p2a -type msms -name smat2a
load mads_p2b -type msms -name smat2b
load mads_d -type msms -name sdna

// center
scene center [.mads]

// generate trace objects
.mads new -type trace -name mcm1 -sel chain=A,B
.mads new -type trace -name mat2 -sel chain=C,D
.mads new -type trace -name dna -sel chain=E,F

// attach surfaces to corresponding parts in .mads
.mads restrict chain=A,B
.smcm1 attach .mads
.mads restrict chain=C
.smat2a attach .mads
.mads restrict chain=D
.smat2b attach .mads
.mads restrict chain=E,F
.sdna attach .mads
.mads restrict

// generate new surfaces
.smcm1 new -name all
.smat2 new -name all
.sdna new -name all
.smat2a new -name all
.smat2b new -name all

// color
.smat2?.all set color=lightgreen
.smat2?.all hide
.sdna.all hide

.smcm1.all set color=yellow -sel $c4
.smcm1.all set color=orange -sel $c6
.smcm1.all set color=red -sel $c8
.smcm1.all set color=red4 -sel $c10

.sdna.all set color=grey50
.sdna.all render t=0.4

.mads.dna render hsc

scene autoslab