Hi Melanie,
funny you ask. Just did this myself a week ago...
To reverse the morph A->B to B->A to create a continuous loop you need a bit
of python scripting, the same for gluing stuff together at the end. This
example needs to be adapted for your needs, but should get you started. For
coloring between the states look at the script “spectrum_states” from the
script repository on the wiki.
HTH
Carsten
##############################################################################
# create objetcs with common residues between the states otherwise rigimol will
bomb
#non working example adjust according to your needs
create ERK_morph, ERK and (resi 339:466,482:497,508:716) and (alt A or alt '')
create ERKP_morph, ERKP and (resi 339:466,482:497,498:716) and (alt A or alt '')
# Eliminate alternate conformations as they are silently rejected in the
alignment or morph
alter EKR_morph, alt=''
alter ERKP_morph, alt=''
# Align the starting structures, the alignment object contains
# matching aligned residues to make sure rigimol stays sane
align ERK_morph, ERKP_morph, object=aln, cycles=0
# create the input structure from the aligned structures
# we begin with the start state
create morph_in, ERK_morph in aln, 1, 1
#
# now add the end-state as state 2
create morph_in, ERKP_morph in aln, 1, 2
#
# now we import the epymol module, this is where
# the rigimol code can be found (incentive only)
from epymol import rigimol
#
# call RigiMOL. Here we ask it to take our 2-state
# object "morph_in", create the morph object,
# use high refinement (10), and not update the PyMOL GUI
# while it thinks (async=0)
rigimol.morph("morph_in", "ERK_2_ERKP", refinement=10, steps=30, async=0)
# Generate the reverse morph by creating a new object and reversing
# the order of states
python
for i in range(1,31):
ts = 31-i
print "Creating state %i" % i
cmd.create("ERKP_2_ERK", "ERK_2_ERKP", source_state=i, target_state=ts)
# add 4 instances of the inital state for final morph
for i in range(1,5):
print "Adding 4 instances of the inital state for final morph: %i" % i
cmd.create("morph", "ERK", source_state=0, target_state=i)
print "Appending all 30 states of ERK->ERKP transition"
cmd.create("morph", "ERK_2_ERKP", source_state=0, target_state=-1)
print "Adding 4 instances of the final state in the middle"
for i in range(1,5):
cmd.create("morph", "ERKP", source_state=0, target_state=-1)
print "Appending all 30 states of ERKP->ERK transition to complete the loop"
cmd.create("morph", "ERKP_2_ERK", source_state=0, target_state=-1)
python end
show cartoon, morph
#show phospotyrosine
show sticks, resn PTR and not (name n,c,o)
From: Melanie Prakash [mailto:melanie.prak...@gmail.com]
Sent: Wednesday, July 29, 2015 8:19 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Phosphorylation
Hi!
Recently, i have been trying to assemble a PyMol video of the phosphorylation
of the MAP kinase ERK from deactivated to activated to deactivated stages.
While I have had success showing the conformational change from inactivated to
activated (using morph mout, 1ERK, 2ERK), not only am I not sure how to
important a phosphate image to show what causes the change, but I also do not
know how to fuse the two morph mout scenes between the deactivated to the
activated and the activated to the deactivated.
Would any of you happen to have any general ideas or some past email
suggestions as to how to solve this? I know I've tried ImageJ (but the quality
is always so poor and i have to make multiple images form my videos and then
fuse them together) as well as a variety of other steps using just the PyMol
program but I haven't found anything.
-Mel
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