Hi Matt,
A Python script can make a chain trace movie with density display that
adds one residue at a time. I've attached an example script and movie.
I used the today's Chimera daily build that has a nice 1-layer
transparency option. That won't work in earlier Chimera versions.
Tom
Matthew Dougherty wrote:
> Hi Tom,
>
> Over the last couple years I have moved my animation off the
> SGI/IrisExplorer to Chimera/Amira.
>
> I have one piece of code on Explorer that I have not moved; attached
> is a typical animation.
>
> what is being accomplished is a demonstration of the folding of a
> protein based on c-alpha backbone and related density.
> starting at the first residue, it proceeds by adding one residue at a
> time.
>
> How would you suggest to move this to chimera?
>
> Matt
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# -----------------------------------------------------------------------------
# Trace C-alpha backbone adding one residue at a time and show simulated map.
#
pdb_path = '/usr/local/src/staff/goddard/pdb/pdb1fav.ent'
resolution = 5.0 # Simulated density resolution, Angstroms
map_color = (.6,.7,.8,.3) # red,green,blue,opacity.
from chimera import runCommand
# Open model
from chimera import openModels as om
m = om.open(pdb_path, 'PDB')[0]
# Orient molecule
runCommand('turn y 90')
runCommand('turn x 30')
# Color molecule and background
runCommand('rainbow')
runCommand('set bg_color white')
# Create residue number label
runCommand('2dlabel create rlab xpos 0.1 ypos 0.9')
# Set display style.
runCommand('repr stick #%d' % m.id)
m.stickScale = 5.0 # Fatter sticks
# Order residues by number and chain id.
rlist = m.residues
rlist.sort(key = lambda r: (r.id.position, r.id.chainId))
# Hide all atoms.
for a in m.atoms:
a.display = False
# Show density adding one residue at a time.
from MoleculeMap import molecule_map
atoms = []
map = None
for r in rlist:
# Accumulate atoms from residue.
atoms.extend(r.atoms)
# Close previous map.
if map:
om.close([map])
# Make map.
map = molecule_map(atoms, resolution, gridSpacing = .2*resolution,
showDialog = False)
map.set_parameters(surface_colors = [map_color],
one_transparent_layer = True)
map.show()
# Display backbone atoms.
for a in r.atoms:
if a.name == 'CA':
a.display = True
# Update residue label
text = 'chain %s residue %d' % (r.id.chainId, r.id.position)
if r.isHelix:
text += ' helix'
elif r.isSheet:
text += ' sheet'
runCommand('2dlabel change rlab text "%s" color black' % text)
# Draw one frame.
runCommand('wait 1')
