Hi Yamei,
If you need to create an (pseudo)atom at a specific location you can write,
pseudoatom objName, pos=[x,y,z]
to specify the position. For example,
pseudoatom testAtom, pos=[15.0, -22.0, 13.5]
Alternatively, if you already have the object, but need to move it you can do,
translate [x,y,z], objectName
For example,
translate [-10, 3, 5.6], myProtein
To get atomic coordinates you can use iterate_state:
iterate_state 1, myObj, print x,y,z
or you can get the indexed chempy model and print its coordinates:
print cmd.get_model("myObj").atom[0].coord
For more information, please check the following pages on the PyMOLWiki:
http://www.pymolwiki.org/index.php/Pseudoatom
http://www.pymolwiki.org/index.php/Translate
http://www.pymolwiki.org/index.php/Iterate_State
Cheers,
-- Jason
On Thu, Aug 11, 2011 at 7:03 PM, Yamei Yu <ymyux...@gmail.com> wrote:
> Hi all,
>
> I remember in pymol you can move an atom to a specific site and use a
> command to get the coordinate of this atom. But I for the name of the
> command. Does any body know?
>
> Thank you!
>
> Yamei
>
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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