[chimerax-users] "Render by attribute" tool in ChimeraX

[Eric Pettersen]

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 at 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
> 
> 
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users