Bouding box dimensions
Hello Thomas, Thank you very much for your help on this. After opening a PDB file, I would like first to display the bounding box of the macromolecule studied. Then, I wish to know the dimensions of the bounding box along its x,y and z axis (in nm or angstrom). How can I do that ? Is the bounding box optimal (i.e. the smallest bounding box surrounding the macromolecule) or defined by a reference frame in the PDB file ? My best regards, Damien ------------------ Damien Larivière, PhD Fourmentin-Guilbert Scientific Foundation France
Hi Damien, Chimera only uses bounding boxes aligned with the PDB file axes. Such bounding boxes are rarely useful for molecules so there is no user interface to display them or measure them. But a few lines of Python code can do it
from chimera import viewer as v v.showBound = True from chimera import openModels as om b = om.bbox()[1] print b.urb - b.llf 26.2573 27.6848 23.0826
Open your PDB file and type these command to the Chimera Python shell (menu Tools / General Controls / IDLE). Or put them in a file with suffix ".cmd" (without the >>> prompt) and open that script in Chimera. The box size output would appear in the reply log (Favorites / Reply log). Tom
Hi Damien, I suggested putting the Python code in a file -- it should have a ".py" suffix, not a ".cmd" suffix as I mistakenly said in the previous email. Tom
participants (2)
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Damien Larivière -
Thomas Goddard