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Contents 1 To-Do 1.1 List of items in "selections" tab of the SAT 1.2 More tools in "selections" tab 1.3 More tools in "representations" tab 1.4 Suggestions for under the Jmol panel

To-Do

Some redesign of the options in the SAT:

List of items in "selections" tab of the SAT

heading	current submenu	current command		proposal submenu	proposal command
	all	all		all	all
protein			Protein
	all protein	protein		all protein
	alpha carbon	alpha		alpha carbon
	backbone/mainchain	backbone		backbone/mainchain	protein and backbone
	helix	helix		sidechain	protein and sidechain
	sheet	sheet		helix
	sidechain	sidechain		sheet
	turn	turn		turn
non-protein			Nucleic acid
	base	base		RNA	rna
	carbohydrate	carbohydrate		DNA	dna
	dna	dna		bases	base
	hetero	hetero		purines	purine
	ions	ions		pyrimidines	pyrimidine
	ligand	ligand		backbone/mainchain	nucleic and backbone
	nucleic	nucleic
	rna	rna	Other
	solvent	solvent		all ligands	ligand
	water	water		solvent/water	solvent
				carbohydrate	carbohydrate
protein residues				all hetero	hetero
	acidic/negative	acidic		ions	ions
	acyclic	acyclic
	aliphatic	aliphatic
	all residues	amino	Protein residues
	aromatic	aromatic	Amino acid properties		maybe "by amino acid property"
	basic/positive	basic		acidic/negative	acidic
	buried	buried		basic/positive	basic
	charged	charged		charged	charged
	cyclic	cyclic		polar	polar
	hydrophobic	hydrophobic		hydrophobic	hydrophobic
	large	large		aromatic	aromatic
	medium	medium
	neutral	neutral
	polar	polar
	small	small
	surface	surface
nucleotides			Nucleic residues		but we can remove this altogether
	dA	dA		dA	dA
	A	A		A	A
	dC	dC		dC	dC
	C	C		C	C
	dG	dG		dG	dG
	G	G		G	G
	dI	dI		dI	dI
	I	I		I	I
	purine	purine		dT	dT
	pyrimidine	pyrimidine		T	T
	dT	dT		dU	dU
	T	T		U	U
	dU	dU
	U	U

More tools in "selections" tab

Add pick from selection to do "select selected and *".

Add clear form to set all text boxes to "all"

More tools in "representations" tab

Add clear form to uncheck all check boxes (next to hide selection button?)

Combine the following items in a new area between the two existing ones: | center selected atoms | center visible atoms | zshade on/off | and the existing slab from above.

Suggestions for under the Jmol panel

Either: number of atoms selected _______

Or: after "Show Selected with Halos", just show the number in parentheses as done in the Jmol right-click menu