5.6: Interactive Molecule and Protein - Reference Options

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Data-* Attribute	What it does	Example	GLmol?	3Dmol?	JSmol?
[required] id	Specifies Molecule using the syntax specified in Table2	data- data-	Yes	Yes	Yes
height	Specifies Height	data-height="100" data-height="80%"	Yes	Yes	Yes
width	Specifies Width	data-width="100" data-width="80%"	Yes	Yes	px only
border	Shows colored border	data-border="true"	Yes	Yes	Yes
label	Shows colored label	data-label="true"	Yes	Yes	Shown by default
spin	Specifies if the molecule should spin	data-spin="true"	Yes	Yes	Not Recommended
multiple	Allows multiple molecules in a row	data-multiple="true"	Yes	Yes	Yes
orbital	Specifies an orbital to display using n, l, & m separated by spaces	data-orbital="4 1 1"	NO	NO	Yes
symmetry	When completed will allow JSmol to calculate symmetry of a molecule	[in development]	NO	NO	In Development

Table 2: Data-id reference table
Prefix Character	Postfix	Example	Database
=	PDB ID	=2POR	RCSB PDB
==	RCSB ligand ID	==HEM	RCSB PDB
$	simple molecule name	$caffeine	NCI NIH
$	SMILES	$CC/C=C/CC	NCI NIH
:	Pubchem CID	:1983	Pubchem
:	InCHI	:BSYNRYMUTXBXSQ-UHFFFAOYSA-N	Pubchem

Table 3: GLmol specific data-attributes
Data attribute name	Description	Choices
colormode	Sets the coloration of the main chain.	[d] chainbow - makes the chain a rainbow * chain - colors each chain differently * b - colors by B factor * polarity - colors by polar/nonpolar * ss - colors by secondary structure
mainchain	Sets the display style of the main chain	[d] thickRibbon * ribbon * strand * chain * cylinderHelix * tube * bonds * none
sidechains	Sets whether side chains will be visible.	[d] false - will not show sidechains * true - will show sidechains
rough-beta	Sets if beta sheets should be rough (not smoothened).	[d] false - will show smooth beta sheets * true - will show roughened beta sheets
hetatm-mode		[d] ballAndStick2 * stick * line * icosahedron * sphere * ballAndStick
base-hetatm-mode	Sets the display style of Nucleic acid bases	[d] line * stick * polygon * none
nonbonded		[d] none * sphere * cross
projectionmode		[d] perspective * orthoscopic
unitcell		[d] false * true
bioassembly		[d] false * true
crystalpacking		[d] false * true
symmetry		[d] false * true
speed	Set rotation speed	[d] 5 * integer

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