[Chimera-users] Worm representation / command line

Eric Pettersen pett at cgl.ucsf.edu
Wed Jul 1 11:28:14 PDT 2015


Hi Xavier,
	No, there's no command line equivalent, nor is there any real plan to add one soon.  Therefore you would have to resort to using a Python script.  It would be a fairly simple script though.  For example, to make a smooth worm whose radius is equal to the residue's MAVconservation attribute + 0.25, it would be something like:

from chimera import openModels, Molecule, RibbonStyleWorm, Residue
for m in openModels.list(modelTypes=[Molecule]:
	for r in m.residues:
		conserve = getattr(r, "MAVconservation", None):
		if conserve is None:
			continue
		r.ribbonDrawMode = Residue.Ribbon_Round
		r.ribbonDisplay = True
		r.ribbonStyle = RibbonStyleWorm(conserve + 0.25)

You would put the above in a file ending in .py (e.g. "worm.py") and run it simply by opening it with the "open" command.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jul 1, 2015, at 1:15 AM, Xavier ROBERT <xavier.robert at ibcp.fr> wrote:

> Dear all,
> 
> I am wondering if there is a way to call "Render by Attribute" at the command line in order to render a worm representation? If not, is this feature planned for the near future and is there any workaround for this?
> 
> Thank you very much in advance.
> Kind regards,
> Xavier R.
> 
> 
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