Jason Vertrees wrote:
> Having said this, you can however, can get the clipping information
> from PyMOL and write scripts against that yourself to determine atom
> inclusion. See get_view (http://www.pymolwiki.org/index.php/Get_View)
> for more help.
>
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 <[email protected]> wrote:
>
>> Hello,
>>
>> I clipped a part of a protein by a slab, by manual, graphical
>> inspection. Now I want to select the slab and store the clipped atoms as
>> new molecule (pdb file), in order to sum up the accessible surface area
>> previously computed by an external program. Unfortunately I didn't find
>> hints, e.g. in the selection algebra
>> (http://www.pymolwiki.org/index.php/Selection_Algebra).
>>
>> Thanks for your advice.
>> Johannes
>>
>>
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