On Mon, Mar 22, 2010 at 4:27 AM, Harry M. Greenblatt
<harry.greenbl...@weizmann.ac.il> wrote:
> BS"D
> Dear Jason,
> I have tried to implement what you suggested, but seeing as I haven't
> made a movie in PyMOL in a long time (and was never very expert at it), I
> don't seem to have got it working. Here is what I did, on my Mac (10.4.11),
> with PyMOL 1.1r1
> I loaded 1yme, which has space group P21.
> I then duplicated it from the Actions menu, and got obj01.
> I then generated symmetry mates within 4 A of 1yme, and displayed only
> 1yme_01000100 since this shows the 2 fold screw axis along b.
> Again, from the actions menu, for obj01 I did Align > To Molecule >
> 1yme_01000100.
> Then I issued the command "mset 1 x120"
> followed by:
> mview store, 1, object=1yme
> frame 60
> matrix_copy obj01, 1yme
> mview store, 60, object=1yme
> I then clicked on play. The movie ran through the 120 frames, but nothing
> happened on the screen.
> So, what did I do wrong?
> Thanks
> Harry
Harry,
I forgot the "matrix_mode" option. Here's a script that should get
your first simple movie done for 1yme and help you with others.
# fetch a protein with a great name
fetch 1yme, one, async=0
# symmetry expand
symexp foo, one, one, 4
# rename for easier use; call it "two"
set_name foo01-100-1,two
# remove others
dele foo*
# setup the camera view
orient
# set up a simple movie and save camera position
mset 1x60
mview store
# save mobile objects original position
mview store, object=one
# align the two objects
align one, two, object=aln
# grab the transformation matrix
mm = cmd.get_object_matrix("one")
# undo the transformation
matrix_reset one
frame 60
# this caused the problems
set matrix_mode, 2
# move object one
cmd.transform_object("one", mm)
# store its new position which
# PyMOL automaticaly reinterpolates for us
mview store, object=one
mplay
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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