Hi Yeping -
To calculate such an angle, you will need two vectors, which you can create
with some pseudoatoms<http://www.pymolwiki.org/index.php/Pseudoatom> and the
orient<http://www.pymolwiki.org/index.php/Orient> command. Before you start,
you should create named selections for the ring and filament.
Step 1: Generate a vector perpendicular to the ring. This method assumes it is
fairly symmetrical.
orient ring_selection # should end up with the view centered on the ring
pseudoatom ring1 # create a pseudoatom at the center of the viewport
translate [0, 0, 10], ring1 # move that pseudoatom 10Å along the viewport
z-axis
pseudoatom ring2 # also at the center of the viewport
distance ring_vector, ring1, ring2 # for display only--make sure it looks
right!
Step 2: Generate a vector parallel to the filament. Assuming the filament is
fairly linear, you can use the same approach. `Orient` should place it along
the viewport X axis. Then place a pair of pseudoatoms and move them left and
right.
orient filament_selection # this should end up being horizontal on the screen
pseudoatom fil1
translate [-10, 0, 0], fil1
pseudoatom fil2
translate [10, 0, 0], fil2
distance filament_vector, fil1, fil2
You could also create pseudoatoms at average positions of a selection at each
end of the filament instead of using `orient`.
Step 3: From the 4 pseudoatoms, you can get 2 vectors by subtracting the
coordinates. Check out Iterate_state for using coordinates in a script.
Step 4: Calculate the angle. I'll also leave it up to you to calculate the
angle once you have the two vectors, but have a look at
http://www.pymolwiki.org/index.php/AngleBetweenHelices or
http://www.pymolwiki.org/index.php/Elbow_angle for some clues.
With all that said, if you don't want to do all of that, you could always just
hold a protractor up to your computer monitor! :)
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Jul 8, 2015, at 10:40 PM, sunyeping
<sunyep...@aliyun.com<mailto:sunyep...@aliyun.com>> wrote:
Dear all,
I have a protein complex which has a ring-like shape; and another protein
complex which forms a long filament. Is there a way in Pymol to measure the
angle between the ring plane and the filament?
Best regards.
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
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