General Pymol Utilities¶
show axes, transform things, etc.
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pymol_util.
corneraxes
(name='axes')[source]¶ DESCRIPTION
Puts coordinate axes to the lower left corner of the viewport.
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pymol_util.
mysetview
(look=Vec( 0.000000, 0.000000, 1.000000 ), up=Vec( 0.000000, 1.000000, 0.000000 ), pos=None, cen=None, ncp=None, fcp=None)[source]¶
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pymol_util.
mkc4
(sel, a=Vec( 1.000000, 0.000000, 0.000000 ), c=Vec( 0.000000, 0.000000, 0.000000 ))[source]¶
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pymol_util.
mkc3
(sel, a=Vec( 0.000000, 0.000000, 1.000000 ), c=Vec( 0.000000, 0.000000, 0.000000 ))[source]¶
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pymol_util.
mkc2
(sel, a=Vec( 0.000000, 0.000000, 1.000000 ), c=Vec( 0.000000, 0.000000, 0.000000 ))[source]¶
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pymol_util.
renumber
(selection='all', start=1, startsele=None, quiet=1)[source]¶ DESCRIPTION
Set residue numbering (resi) based on connectivity.ARGUMENTS
selection = string: atom selection to renumber {default: all}
start = integer: counting start {default: 1}
startsele = string: residue to start counting from {default: first in selection}
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pymol_util.
color_obj
(rainbow=0)[source]¶ AUTHOR
Gareth StockwellUSAGE
color_obj(rainbow=0)
This function colours each object currently in the PyMOL heirarchy with a different colour. Colours used are either the 22 named colours used by PyMOL (in which case the 23rd object, if it exists, gets the same colour as the first), or are the colours of the rainbow
SEE ALSO
util.color_objs()
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pymol_util.
make_zdock_set
(d='/work/sheffler/Dropbox/project/zdock/pdb_lib', tgt='/work/sheffler/data/zdock_AB')[source]¶
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pymol_util.
make_inputs_from_cb_only
(d='/work/sheffler/Dropbox/test/silva/run_resl_6/', tgt='/work/sheffler/tmp/asym_iface')[source]¶
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pymol_util.
cube
(lb=Vec( -10.000000, -10.000000, -10.000000 ), ub=Vec( 10.000000, 10.000000, 10.000000 ), r=0.5, xform=Xform( Mat( Vec( 1.000000, 0.000000, 0.000000 ), Vec( 0.000000, 1.000000, 0.000000 ), Vec( 0.000000, 0.000000, 1.000000 ) ), Vec( 0.000000, 0.000000, 0.000000 ) ))[source]¶
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pymol_util.
getrelframe
(newobj, refobj, Forigin=None)[source]¶ get transform between two objects, assume the obj’s are identical