Below is a variant of camera_travel (as Pythonised by Lieven Buts) which takes an explicit final view matrix as an argument rather than a PyMol selection as in the original version. This allows you to specify the exact view you want, rather than relying on the combination of PyMol 'orient' and 'zoom' command to generate it for you. This is particularly useful for defining a base view to which you can return.
For those with tricky E-mail clients the routine is also attached as a text file.
Cheers,
Laurence
def camera_view_travel(first,nframes=30,new_view=(\
1.000000000, 0.000000000, 0.000000000,\
0.000000000, 1.000000000, 0.000000000,\
0.000000000, 0.000000000, 1.000000000,\
0.000000000, 0.000000000, -50.000000000,\
0.000000000, 0.000000000, 0.000000000,\
40.000000000, 100.000000000, 0.000000000 )):
"""
Generate progressive view matrices to move the camera smoothly
from the current view to a new view provided as an argument.
first - start frame
nframes - duration
new_view - PyMol view matrix that defines the view at the end
of the sequence
"""
try:
first=int(first)
except:
print "camera_travel: first frame must be an integer"
return -1
try:
nframes=int(nframes)
except:
print "camera_travel: number of frames"
ff=float(1.0/nframes)
old_view = cmd.get_view(2)
# print ( "view : (" + "%8.3f, "*17 + "%8.3f)" ) % (old_view)
# print "oldtran : %8.3f %8.3f %8.3f" % (old_view[12],
old_view[13], old_view[14])
# capture new zoom/clip parameters
ozc1 = new_view[11]
ozc2 = new_view[15]
ozc3 = new_view[16]
# calculate shift in zoom/clip parameters
dzc1 = (ozc1 - old_view[11]) * ff
dzc2 = (ozc2 - old_view[15]) * ff
dzc3 = (ozc3 - old_view[16]) * ff
ozc1 = old_view[11]
ozc2 = old_view[15]
ozc3 = old_view[16]
# capture new translation vector component
ox = new_view[12]
oy = new_view[13]
oz = new_view[14]
# calculate shift vector
dx = ox - old_view[12]
dy = oy - old_view[13]
dz = oz - old_view[14]
dx = dx*ff
dy = dy*ff
dz = dz*ff
ox = old_view[12]
oy = old_view[13]
oz = old_view[14]
# capture old and new rotation matrix components in quaternion
form
# m[0][0] = v[0] m[0][1] = v[1] m[0][2] = v[2]
# m[1][0] = v[3] m[1][1] = v[4] m[1][2] = v[5]
# m[2][0] = v[6] m[2][1] = v[7] m[2][2] = v[8]
qx1,qy1,qz1,qw1 = quaternion(old_view)
qx2,qy2,qz2,qw2 = quaternion(new_view)
# calc cosine
cosom = qx1 * qx2 + qy1 * qy2 + qz1 * qz2 + qw1 * qw2
limit = 0.001
if cosom>1.0+limit:
raise ValueError,"Cosine of omega way out of range (positive)"
elif cosom>1.0:
print "Warning: cosom corrected from ",cosom,"to",
cosom = 1.0
print cosom
if cosom<-1.0-limit:
raise ValueError,"Cosine of omega way out of range (negative)"
elif cosom<-1.0:
print "Warning: cosom corrected from ",cosom,"to",
cosom = 1.0
print cosom
# adjust signs
if (cosom < 0.0):
cosom = -cosom
to0 = -qx2
to1 = -qy2
to2 = -qz2
to3 = -qw2
else:
to0 = qx2
to1 = qy2
to2 = qz2
to3 = qw2
# calc coefficients
omega = acos(cosom)
sinom = sin(omega)
if sinom==0.0:
sinom=limit
print "Warning: sinom corrected!"
# restore old view
cmd.set_view( ("%8.3f, " * 17 + "%8.3f") % tuple(old_view) )
# loop interpolating over nframes generating interpolated
quaternion
for a in range(nframes+1):
scale0 = sin((1.0 - float(a*ff)) * omega) / sinom
scale1 = sin(float(a*ff) * omega) / sinom
rx = scale0 * qx1 + scale1 * to0;
ry = scale0 * qy1 + scale1 * to1;
rz = scale0 * qz1 + scale1 * to2;
rw = scale0 * qw1 + scale1 * to3;
# convert back to matrix
x2 = rx + rx
y2 = ry + ry
z2 = rz + rz
xx = rx * x2
xy = rx * y2
xz = rx * z2
yy = ry * y2
yz = ry * z2
zz = rz * z2
wx = rw * x2
wy = rw * y2
wz = rw * z2
nv0 = 1.0 - (yy + zz)
nv3 = xy - wz
nv6 = xz + wy
nv1 = xy + wz
nv4 = 1.0 - (xx + zz)
nv7 = yz - wx
nv2 = xz - wy
nv5 = yz + wx
nv8 = 1.0 - (xx + yy)
# update translation vector
ox = ox + dx
oy = oy + dy
oz = oz + dz
# update zoom/clip parameters
ozc1 = ozc1 + dzc1
ozc2 = ozc2 + dzc2
ozc3 = ozc3 + dzc3
cmd.mdo("%d" % (first), ("set_view (" + "%8.3f, "*17 +
"%8.3f)") %
(nv0,nv1,nv2,nv3,nv4,nv5,nv6,nv7,nv8,old_view[9],old_view[10],ozc1,
ox,oy,oz,ozc2,ozc3,old_view[17]))
first += 1
cmd.set_view( ("%8.3f, "*17 + "%8.3f") %
(nv0,nv1,nv2,nv3,nv4,nv5,nv6,nv7,nv8,old_view[9],old_view[10],ozc1,
ox,oy,oz,ozc2,ozc3,old_view[17]))
camera_view_travel.py
Description: Binary data
------------------------------------------------------------------------ --
Laurence H. Pearl Section of Structural Biology, Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK Phone +44-207-970 6045 : Secretary +44-207-970 6046 FAX +44-207-970 6051 : E-Mail laurence.pe...@icr.ac.uk------------------------------------------------------------------------ --
" Live Simply and do Serious Things .. " - Dorothy Crowfoot Hodgkin------------------------------------------------------------------------ --
