Hi Francesco, You will have to resort to a tiny bit of Python in order to set the atomic radii to be the same as the bfactors. Open ChimeraX's Python shell (Tools→General→Shell) and, assuming that the structure is the only model open, type:
atoms = session.models[0].atoms atoms.radii = atoms.bfactors
After that you should be able to use the normal "surface" and "measure volume" commands to create the surface and measure its volume.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jul 6, 2021, at 9:06 AM, Francesco Musiani via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX developers, I would like to use one feature from the old "render by attribute" tool present in Chimera.
My aim is to adapt the atomic radius of a series of atoms according to the value written in the B-factor column of the PDB file. Then I would like to calculate the molecular surface of the resulting molecule in order to calculate the surface volume. Chimera can do the first part by using "render by attribute" tool, but unfortunately it fails in the creation of the surface of the resulting molecule. How can I achieve the same result by using ChimeraX?
Thanks in advance.
Francesco
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