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SelectClipped - Revision history
2026-04-05T05:11:35Z
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2014-03-28T03:49:39Z
<p>2 revisions</p>
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Bell
https://wiki.pymol.org/index.php?title=SelectClipped&diff=9713&oldid=prev
Speleo3: select_clipped command
2011-08-30T15:21:58Z
<p>select_clipped command</p>
<p><b>New page</b></p><div>This script selects those atoms that are between the near and far [[clip|clipping plane]].<br />
<br />
== Usage ==<br />
<br />
select_clipped [name [, selection [, state]]]<br />
<br />
== The Code ==<br />
<source lang="python"><br />
from pymol import cmd<br />
<br />
def clipped_by(at,v):<br />
x,y,z = at.coord<br />
nz = v[2]*(x-v[12])+v[5]*(y-v[13])+v[8]*(z-v[14])-v[11]<br />
return nz > v[15] and nz < v[16]<br />
<br />
def clipped(selection="all",state=1):<br />
v = cmd.get_view()<br />
return [ i.id for i in cmd.get_model(selection,state).atom if clipped_by(i,v) ]<br />
<br />
def select_clipped(name='clipped', selection='all', state=1):<br />
'''<br />
DESCRIPTION<br />
<br />
Select atoms between clipping planes<br />
<br />
USAGE<br />
<br />
select_clipped [name [, selection [, state]]]<br />
'''<br />
state = int(state)<br />
cmd.select(name, 'none')<br />
for model in cmd.get_object_list('(' + selection + ')'):<br />
cmd.select_list('__tmp', model, clipped('(%s) and (%s)' % (model, selection), state))<br />
cmd.select(name, '__tmp', merge=1)<br />
cmd.delete('__tmp')<br />
<br />
cmd.extend('select_clipped', select_clipped)<br />
</source><br />
<br />
To use this script save it to "clipped.py". Then load the script from PyMOL ("run clipped.py").<br />
<br />
== Example ==<br />
<br />
<source lang="python"><br />
# for example, fetch 1cll<br />
<br />
fetch 1cll, async=0<br />
<br />
# orient it to clip out some data<br />
<br />
set_view (\<br />
-0.555155039, 0.671998382, 0.490123481,\<br />
0.050991829, 0.615659416, -0.786360741,\<br />
-0.830182374, -0.411559790, -0.376052886,\<br />
0.000000000, 0.000000000, -188.930786133,\<br />
13.649702072, 25.646595001, 12.279129982,\<br />
172.813293457, 205.048278809, -20.000000000 )<br />
<br />
# run the script<br />
<br />
select_clipped 1cllClipped, 1cll<br />
<br />
# setup the view<br />
<br />
orient<br />
<br />
# remove the surface flag on these atoms<br />
<br />
flag exfoliate, 1cllClipped<br />
<br />
# show everything as sticks<br />
<br />
show sticks<br />
<br />
# show those atoms not exfoliated as surface<br />
<br />
show surface<br />
</source><br />
<br />
[[Category:Script_Library]]<br />
[[Category:ObjSel_Scripts]]</div>
Speleo3