Hi Marcelo -
Is Object 2 actually a pseudoatom? Or, if not, can it be placed separately
from Object 1? If either of those are the case, it would be much easier to
place the pseudoatom at a point equidistant from the two ends of Object 1 than
mess with rotation matrices, etc. Here’s what I worked out.
# get a long protein, e.g. collagen
fetch 1bkv, async=0
as cartoon
# place a couple helper pseudoatoms at the "ends" of the collagen
(approximately)
pseudoatom nterm, resi 2+31+61, vdw=2
pseudoatom cterm, resi 30+60+90, vdw=2
select ends, nterm or cterm
show spheres, ends
# orient the helper pseudoatoms along one of the display axes (usually ends up
being x)
orient ends
# place another helper pseudoatom at the "midpoint" of the object
pseudoatom obj_b, ends, vdw=4
show spheres, obj_b
# move it (e.g.) 50Å away
translate [0,0,-50], obj_b
# make sure it looks right
orient ends or obj_b
You could then load your “real” Object 2 (if necessary) and move it to the
obj_2 pseudoatom using a combination of `origin` and the COM script
(http://www.pymolwiki.org/index.php/Com), for example. Haven’t tested that,
but it should be possible.
Hope that helps!
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Apr 28, 2015, at 1:57 PM, Marcelo Marcet
<mmar...@nait.ca<mailto:mmar...@nait.ca>> wrote:
Hi Pymol Users,
I have 2 objects (objects 1 and 2) and I would like to re-orient object 1 so
that the distance from either end of object 1 becomes the same to object 2 (see
image). Is there a way to achieve this in PyMol?
I have tried using the mouse in edit mode and I have tried using the
rotate/translate commands. Neither method can move object 1 without altering
the position of the lower end of object 1.
Regards,
Marcelo
<image.jpeg>
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