Help:Viewing pages
From Proteopedia
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==Using the console== | ==Using the console== | ||
| - | The console is a way to pass any command to Jmol. As a casual user of Jmol, you only need to know a handful of commands not available through the menu. If you become a frequent user of Jmol, you might stop using the menu and type commands instead once you are familiar with them. | + | The console is a way to pass any command to Jmol. As a casual user of Jmol, you only need to know a handful of commands not available through the menu. If you become a frequent user of Jmol, you might stop using the menu and type commands instead once you are familiar with them. To open the console, use the menu item "Console". Try it. |
| - | + | ||
*Finding a residue: If you want to find a specific residue in a structure and you know the residue number, say residue 72, type "center 72" in the console. You can also select it by typing "select 72", and then change how it is represented in the 3D figure by using the menu. | *Finding a residue: If you want to find a specific residue in a structure and you know the residue number, say residue 72, type "center 72" in the console. You can also select it by typing "select 72", and then change how it is represented in the 3D figure by using the menu. | ||
*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 33" to add residue 33 to your selection. You can also select multiple parts of the structure in a single command like "select (42, 67, 82) and side chain 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 33" to add residue 33 to your selection. You can also select multiple parts of the structure in a single command like "select (42, 67, 82) and side chain 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 backbone 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 backbone and helix"), then type "hbonds calculate" in the console. This will calculate possible hydrogen bonds and display them. | ||
| + | *Increasing the size of labels shown when hovering: When giving a presentation and projecting a page, the "hover labels" are sometimes too small and too complicated to be appreciated by the viewers. A command like | ||
| + | <nowiki>hover "%n%R %a"; font hover 30</nowiki> | ||
| + | will help. | ||
</StructureSection> | </StructureSection> | ||
==External links== | ==External links== | ||
Revision as of 16:16, 16 October 2018
This is a brief tutorial on how to read a Proteopedia article and view the integrated 3D figures.
Example structure: Lysozyme
In this tutorial, we will use lysozyme bound to a as our example structure. In the , the protein is shown in blue ("deep sky blue", to be exact) as a carbon alpha trace, and the carbohydrate is shown in all-bonds, colored using the CPK color scheme. Lysozyme was the first enzyme structure to be solved.
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