[Chimera-users] Define centroid issue

Francesco Pietra chiendarret at gmail.com
Wed May 8 00:16:45 PDT 2013


I was unable to put to work

define centroid radius 0.5 color red :ligand_residue_name


define centroid radius 0.5 color red #0&@serialNumber=1972

with a homodimeric protein (I am at CHARMM NAMD/XPLOR, so that the two
subunits are only distinguished by either the atom sequential number or the
segment name, the latter not being understood by chimera, as far as I
know). In the first case, running the movie after the appropriate further
steps, the centroid sequence obtained was for the centroid between the two
protein ligands, as it  was expected.

In the second case (as I wanted to refer to the ligand in subunit A only),
the command raised the error:
AttributeError: 'NoneType' object has no attribute 'openState'

  File "/opt/UCSF/Chimera64-1.7/share/StructMeasure/Geometry.py", line 293,
in _getRefInfo
    invXForm = lowest.openState.xform

Please notice that the line command


correctly selects the ligand on subunit A (a diatomic ligand, where "1972"
is the sequential number of one of the two atoms of the ligand. Here "#0"
may be redundant, as it deals of a single model. However, using
"@serialNumber=1972" raised the same error.

I fear I am missing some obvious facet of define centroid, so that I thank
you for your patience.

francesco pietra
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