Hi Johannes,
Coincidentally, I found myself in need of the same functionality the
other day. I came up with this:
####
from pymol import cmd
def clipped_by(at,v):
x,y,z = at.coord
nz = v[2]*(x-v[12])+v[5]*(y-v[13])+v[8]*(z-v[14])-v[11]
return nz > v[15] and nz < v[16]
def clipped(selection="all",state=1):
v = cmd.get_view()
return [ i.id for i in cmd.get_model(selection,state).atom if
clipped_by(i,v) ]
####
The function 'clipped' returns a list of IDs for atoms from a given
selection that are outside the clipping planes. You can use it like:
run clipped.py
fetch 3lzt,async=0
clip near,-30
cmd.select_list("clipsed","3lzt",clipped("3lzt"))
orient
hide
show spheres, not clipsed
Hope it helps,
Tsjerk
On Wed, Mar 2, 2011 at 5:27 PM, Johannes Wollbold <jwollb...@gmx.de> wrote:
> Hi,
>
> I implemented the coordinate transformation and the selection of atoms
> outside PyMol, in R. In principle it works, but there seems to be some
> error, since too many atoms are selected, corresponding roughly, but not
> completely to an enlarged clipping corridor between the planes defined by
> get_view, matrix elements (6,1) and (6,2). Or could it be that not the
> complete slab is visualized in PyMol? However, the missing atoms are
> completely shadowed.
>
> Do I understand the rows of the view matrix well (see
> http://www.pymolwiki.org/index.php/Get_View), by computing the following
> coordinate transformation?:
> 1) Translation of the original pdb coordinates by subtracting row 5 of the
> view matrix (translation of the coordinate origin to the rotation center).
> 2) Rotation of the coordinates by rows 1-3 of the view matrix.
> 3) Test: view[4,3] + view[6,1]) <= z <= view[4,3] + view[6,2].
>
> Sorry for this simple question of affine geometry, but I hope I did not make
> a logical mistake in this domain...
>
> Regards
> Johannes
>
>
> Tsjerk Wassenaar wrote:
>
> Hi Johannes,
>
> It's not that hard. The clipping planes are defined by the z coordinate (in
> the viewing matrix). So you can get the atoms for a selection, transform to
> get the new z coordinate only, and check whether it's in between the planes:
>
> m = cmd.get_model(selection).atom
> v = cmd.get_view()
> m = [ i for i in m if clipped(i,v) ]
>
> So clipped should do the transform and check whether the atom is clipped.
> The trick then is to turn m back into a selection.
>
> Hope it helps,
>
> Tsjerk
>
> On Feb 25, 2011 5:18 PM, "Johannes Wollbold" <jwollb...@gmx.de> wrote:
>
> Jason Vertrees wrote: > Having said this, you can however, can get the
> clipping information > from P...
>
> Hi Jason,
>
> thank you again for the hint. First I looked if I can select atoms
> according to their coordinates, or store new coordinates after a
> rotation / shift. But implicitly you already said that such
> functionalities are not yet implemented. If clipping is performed with
> the original camera view, the task is simple. get_view gives the output
> (see above link to the help page):
>
> set_view (\
> 1.000000000, 0.000000000, 0.000000000,\
> 0.000000000, 1.000000000, 0.000000000,\
> 0.000000000, 0.000000000, 1.000000000,\
> 0.000000000, 0.000000000, -320.337890625,\
> 74.147140503, 74.174217224, 74.123344421,\
> 317.145324707, 323.530487061, -20.000000000 )
>
> According to (4,3), the camera is shifted by -320 A in z direction only.
> Since (6,1) and (6,2) indicate the camera distances of the slab planes,
> I can select, in the pdb file, the atoms with (74 - 320 + 317 ) <= z <=
> (74 - 320 + 323).
>
> For different views, coordinate transformations with the rotation matrix
> of the first 3 lines are needed. This should not be very difficult, but
> perhaps somebody has already a solution?
>
> Best regards
> Johannes
>
>> On Thu, Feb 24, 2011 at 3:50 AM, Johannes Wollbold <jwollb...@gmx.de>
>> wrote: > >> Hello, >> >>...
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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