Re: [PyMOL] moving objects

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 <MM...@na...<mailto:MM...@na...>> 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>
------------------------------------------------------------------------------
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y_______________________________________________
PyMOL-users mailing list (PyM...@li...)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pym...@li...