[Chimera-users] Auto-associate define attribute/render by attribute

[Eric Pettersen]

> On Nov 27, 2019, at 1:07 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Python is beyond my skill set, though… somebody else would have to advise on that.


The first thing I should say is that Multalign Viewer is only available as a graphical tool, so you will only be able to script this for a Chimera that is running its graphical interface, not in any headless “batch” mode.  Okay, with that out of the way, the first job is to get a Python instance of Multalign Viewer showing the sequence you want with the chains you want associated.  Unlike ChimeraX, which associates on a per-chain basis, Chimera associates on a per-structure basis, so you will have to first split your structure apart by chains (with the “split” command).  If you have the pertinent sequence in a file, you could do this:

	from MultAlignViewer.MAViewer import MAViewer
	mav = MAViewer(“full-path-to-sequence-file”)

If you don’t have a file, but you know you want to use the sequence of chain C, you could do this:

	from chimera import openModels, Molecule
	for m in openModels.list(modelTypes=[Molecule]):
		try:
			seq = m.sequence(‘C’)
		except KeyError:
			continue
	from MultAlignViewer.MAViewer import MAViewer
	mav = MAViewer([seq])

You then add your custom header file with:

	mav.readHeaderFile(“full-path-to-header-file”)

After that, the residues will have the necessary attribute (prefixed with “mav”, so if the header attribute is ChouFasmanImmuno, the residue attribute is mavChouFasmanImmuno).

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab



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