[Chimera-users] Define centroid issue

Elaine Meng meng at cgl.ucsf.edu
Wed May 8 09:44:01 PDT 2013

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.

(c) the correct specification of attributes like serialNumber is with "/" e.g. @/serialNumber=1972 

(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 hope this helps,
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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