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<StructureSection load='' size='500' side='right' caption='Caption for this structure' scene='79/797412/Overall/1'> | <StructureSection load='' size='500' side='right' caption='Caption for this structure' scene='79/797412/Overall/1'> | ||
</StructureSection> | |||
==Using the mouse== | ==Using the mouse== | ||
*Identifying atoms: Make sure the molecule is not spinning on its own (you can turn that off in the 3D browser by clickling the "+/- spin" text on the bottom). Then, hover (i.e. point with the mouse pointer without moving or clicking) over an atom, and a small pop-up text will appear. Try it. Something like "[ALA]23:A.CA #252" should have appeared, which would tell you this atom is part of an alanine residue with residue number 23 of chain (or subunit) A. The atom is an alpha carbon (CA) and is atom number 252 in the coordinate file. | *Identifying atoms: Make sure the molecule is not spinning on its own (you can turn that off in the 3D browser by clickling the "+/- spin" text on the bottom). Then, hover (i.e. point with the mouse pointer without moving or clicking) over an atom, and a small pop-up text will appear. Try it. Something like "[ALA]23:A.CA #252" should have appeared, which would tell you this atom is part of an alanine residue with residue number 23 of chain (or subunit) A. The atom is an alpha carbon (CA) and is atom number 252 in the coordinate file. | ||
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*Selecting multiple parts of the molecule: When using the menu to select, each new selection command cancels the old one. Using the console, you can type something like "selected selected and 433" to add residue 433 to your selection. You can also select multiple parts of the structure in a single command like "select (42, 67, 82) and sidechain and _C", which would select all carbon atoms in the side chain of residues 42, 67 and 82. You can learn common selection command in this [http://cbm.msoe.edu/includes/modules/jmolTutorial/jmolSelect.html tutorial]. The complete set of selection commands is explained in the Jmol manual. | *Selecting multiple parts of the molecule: When using the menu to select, each new selection command cancels the old one. Using the console, you can type something like "selected selected and 433" to add residue 433 to your selection. You can also select multiple parts of the structure in a single command like "select (42, 67, 82) and sidechain and _C", which would select all carbon atoms in the side chain of residues 42, 67 and 82. You can learn common selection command in this [http://cbm.msoe.edu/includes/modules/jmolTutorial/jmolSelect.html tutorial]. The complete set of selection commands is explained in the Jmol manual. | ||
*Showing hydrogen bond: Select the entire structure or parts you are interested in (e.g. "select mainchain and helix"), then type "hbonds calculate" in the console. This will calculate possible hydrogen bonds and display them. | *Showing hydrogen bond: Select the entire structure or parts you are interested in (e.g. "select mainchain and helix"), then type "hbonds calculate" in the console. This will calculate possible hydrogen bonds and display them. | ||