[Chimera-users] Define centroid issue

Francesco Pietra chiendarret at gmail.com
Wed May 8 11:05:28 PDT 2013

On Wed, May 8, 2013 at 6:44 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Francesco,
> it is impossible to test without the file, but here are some points:
> (a) if there are indistinguishable atoms, it is generally considered an
> error of the input file
> (b) you said subunit A... if there are chain IDs A and B in the file, you
> could use those in the specification, for example ":RES.A" if RES is the
> residue name.  However, maybe that is just your terminology and chains
> weren't marked in the file.
Sorry for the misleading words I used. I said chains A/B by referring to
the original PDF file from the PDB bank. However, as I said, I built the
model of the homodimer for NAMD/XPLOR, whereby the chain labels as well as
residues names and numbers are the same for both chains (luckily so, as it
avid the headaches of using the AMBER language for multimers). Every group
of atoms, be them proteins or ligands, or what else, is distinguished by
either the "segment name" or atom ID.

My silly mistake was

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

without the backslash (which I used by simply selecting  the atom). Now the
trace of the centroid comes out cleanly.

(c) the correct specification of attributes like serialNumber is with "/"
> e.g. @/serialNumber=1972
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
> >
> <
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors
> >
> (d) it doesn't really make sense to define centroid of one atom, you would
> just get the coordinates of that atom (which you could already do using
> command "getcrd").  Maybe that was just an example and you were really
> going to use a range of serial numbers, for example:
> define centroid color red radius .5 @/serialNumber>30 and serialNumber<80

I'll consider that. Although it deals - as I said - of a diatomic ligand ,
it is better to point to the center of mass of the ligand.

Thank a lot for your kind help.

francesco pietra

> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On May 8, 2013, at 12:16 AM, Francesco Pietra wrote:
> > Hello:
> > I was unable to put to work
> >
> > define centroid radius 0.5 color red :ligand_residue_name
> >
> > or
> >
> > 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
> >
> > #0&@serialNumber=1972
> >
> > 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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