# Bob Hanson 12:11 AM 5/25/2008

zap
#set loglevel 5
set appendnew false
set pdbSequential true
set drawpicking true
set perspectivedepth off

data "mydata"
ATOM      1  N   GLY A   0       0.000  1.5000  0.0000  1.00 22.43           N  
ATOM      2  CA  GLY A   0       0.000  0.0000  0.0000  1.00 23.58           CA  
ATOM      3  C   GLY A   0       1.500  0.0000  0.0000  1.00 25.04           C
ATOM      4  O   GLY A   0       2.500  -.5000  0.0000  1.00 22.70           O  
end "mydata"

# set the random rotations:

cant = "{" + random(-1,1) + " " + random(-1,1) + " " + random(-1,1) + "}"
degCant = random(10,170);

rot = "{" + random(-1,1) + " " + random(-1,1) + " " + random(-1,1) + "}"
degRot = random(10,170)


cant = cant/cant
rot = rot/rot
print "cant=" +cant + " " + degCant
print "rot=" + rot + " " + degRot

# loop through and build structure
rscant = "rotateSelected internal " + degCant + " {0 0 0} " + cant
for (var i = 0; i < 24; i = i + 1);
 # translate and rotate what we have now

 select *;
 translateSelected {0 0 1}
 rotateSelected internal {0 0 0} @rot @degRot

 # save the current set

 select *;
 var a = {selected}

 # add the new coordinates

 sdata = data("mydata")
 sdata = sdata.replace("  0   ",("  "+(i + 1))[-2][0] + "   ")
 #print sdata
 data "append @sdata"

 # set at a canter only the new coordinates

 select not @a
 script inline @rscant

 # iterate

end for

# save the structure and reload it to create the polymers

select *
write pdb "tqall.pdb"
load "tqall.pdb"

# set the view

axes molecular; axes on
wireframe 0.05
center visible
spacefill off

# add the comment at the top

set echo top left
var e = "cant="+cant + "/" + degCant + "|rot = " + rot + "/" + degRot
echo @e

# make the quaternion and label by atominDex

quaternion
select visible
label %D
trace off

# display axes

#var y = cant * 10 * sin(degCant/2)
#draw vCant VECTOR {0 0 0} @y ">cant" color yellow

var y = rot * 10 * sin(degRot/2)
draw vRot VECTOR {0 0 0} @y ">rot" color red
print y

# create the ellipse as a pancake ellipsoid

var index1 = {2.1}[1].atomIndex
var index2 = {2.1}[2].atomIndex

var atom1 = {atomindex = index1}.xyz
var atom2 = {atomindex = index2}.xyz

perp = cross(atom1,atom2)
perp = perp/perp * 10


minor = cross(perp,rot)
major = cross(perp,minor)
major = major/major * 10
rmdeg = angle(major,{0 0 0},rot)
minor = minor/minor * 10 * sin(rmdeg)

draw vPerp arrow {0 0 0} @perp ">perp"
draw vMinor arrow {0 0 0} @minor ">minor"
draw vMajor arrow {0 0 0} @major ">major"

perp = perp/50
ellipsoid myellipse axes @major @minor @perp

# go to the model

model
axes molecular

# draw the rotational vector

var y = rot * 10
draw axisRot VECTOR {0 0 0} @y ">rot" color red

# Now create and run the script for the frame arrows

write quaternion s "tq.spt"
script "tq.spt"
write jpg "qm.jpg"
quaternion
write jpg "qq.jpg"
write state "qtest_last.spt"