#!/usr/local/bin/vmd
#Emad Tajkhorshid
# VMD demo script for GlpF demo presentation, which is designed 
# for more general purposes/people. It is less scientific and only
# describes the size of the system, water channels in general, and
# gives a brief introduction for IMD on glycerol pulling

# Defining new materials used for controlling the visibility of 
# different elements

#material add protein
#material change ambient protein 0.000000
#material change specular protein 1.000000
#material change diffuse protein 0.650000
#material change shininess protein 0.534020
#material change opacity protein 1.000000

material add pro2tube
material change ambient pro2tube 0.000000
material change specular pro2tube 1.000000
material change diffuse pro2tube 0.650000
material change shininess pro2tube 0.534020
material change opacity pro2tube 1.000000

material add waterfile
material change ambient waterfile 0.000000
material change specular waterfile 1.000000
material change diffuse waterfile 0.650000
material change shininess waterfile 0.534020
material change opacity waterfile 1.000000

material add off
material change ambient off 0.000000
material change specular off 1.000000
material change diffuse off 0.650000
material change shininess off 0.534020
material change opacity off  0.000000

set viewplist {}
set fixedlist {}

# First we need a tetramer filled with water
# Because the introduction starts with the role of these channels
# in water transport

mol load pdb tetramer.pdb 
mol delrep 0 0

# rep 0 PROTEIN
mol representation off
mol color SegName
mol selection {protein and not hydrogen and backbone and not name O}
mol addrep 0

# rep 1 BULK WATER
mol representation Off
mol color Name
mol selection {water and (z > 12 or z < -10) }
mol addrep 0

# rep 2 LIPIDS
mol representation Off
mol color ColorID 3
mol selection {resname POPE and not hydrogen}
mol addrep 0

# rep 3 GLYCEROLS if any
mol representation Off
mol color Name
mol selection {resname GCL}
mol addrep 0

# rep 4
mol representation Off
mol color Name
mol selection {(water and same residue as (x < 17 and x > 11 and y < -10 and y > -17 and within 3 of segname PRO2))}
mol material waterfile
mol addrep 0
mol rename top {tetramer.pdb:000}
set viewpoints([molinfo top]) {{{1.000000 0.000000 0.000000
-15.161256} {0.000000 1.000000 0.000000 16.054396} {0.000000 0.000000
1.000000 -0.711284} {0.000000 0.000000 0.000000 1.000000}} {{0.999494
0.028310 0.014524 0.000000} {0.013160 0.047812 -0.998769 0.000000}
{-0.028970 0.998455 0.047415 0.000000} {0.000000 0.000000 0.000000
1.000000}} {{0.013138 0.000000 0.000000 0.000000} {0.000000 0.013138
0.000000 0.000000} {0.000000 0.000000 0.013138 0.000000} {0.000000
0.000000 0.000000 1.000000}} {{1.000000 0.000000 0.000000 0.220000}
{0.000000 1.000000 0.000000 -0.010000} {0.000000 0.000000 1.000000
0.000000} {0.000000 0.000000 0.000000 1.000000}}}
lappend viewplist [molinfo top]
# done with molecule 0



# Now we load a monomer for detailed description of the monomer

mol load pdb monomer.pdb
mol delrep 0 1

# rep 0 full protein
mol representation Off
mol color ColorID 1
mol selection {all}
mol material pro2tube
mol addrep 1

# rep 1 NPA notifs
mol representation Off
mol color Name
mol selection {(resid 68 203) and not name HB1 HB2 HA HN}
mol material Opaque
mol addrep 1

# rep 2 inverted helices
mol representation Off
mol color ColorID 7
mol selection {resid 64 to 68 199 to 203 }
mol addrep 1

# rep 3 helices
mol representation Off
mol color ColorID 0
mol selection {resid 68 to 78 203 to 217}
mol addrep 1

# rep 4 selectivity filter
mol representation Off
mol color Name
mol selection {resid 48 200 206 and not hydrogen}
mol addrep 1

# rep 5 Carbonyl groups 
mol representation Off
mol color Name
mol selection {resid 64 65 66 199 200 201 and name C O}
mol addrep 1


mol rename top {monomer.pdb:001}
set viewpoints([molinfo top]) {{{1.000000 0.000000 0.000000
-15.161256} {0.000000 1.000000 0.000000 16.054396} {0.000000 0.000000
1.000000 -0.711284} {0.000000 0.000000 0.000000 1.000000}} {{0.999494
0.028310 0.014524 0.000000} {0.013160 0.047812 -0.998769 0.000000}
{-0.028970 0.998455 0.047415 0.000000} {0.000000 0.000000 0.000000
1.000000}} {{0.013138 0.000000 0.000000 0.000000} {0.000000 0.013138
0.000000 0.000000} {0.000000 0.000000 0.013138 0.000000} {0.000000
0.000000 0.000000 1.000000}} {{1.000000 0.000000 0.000000 0.220000}
{0.000000 1.000000 0.000000 -0.010000} {0.000000 0.000000 1.000000
0.000000} {0.000000 0.000000 0.000000 1.000000}}}
lappend viewplist [molinfo top]
set topmol [molinfo top]
# done with molecule 1

foreach v $viewplist {
  molinfo $v set {center_matrix rotate_matrix scale_matrix
global_matrix} $viewpoints($v)
}
foreach v $fixedlist {
  molinfo $v set fixed 1
}
unset viewplist
unset fixedlist
mol top $topmol
unset topmol

source buttons.tcl
menu graphics on
display projection orthographic
axes location off