Difference between revisions of "Features since version 10"
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Jmol + JSmol Documentation
(summarized new stuff in version 10.2) |
(added link to changelog on sourceforge website) |
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{{Jmol_Documentation_Sections}} | {{Jmol_Documentation_Sections}} | ||
| − | + | == New in version 10.2 == | |
| + | [http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-10.2/new.htm click here] for interactive examples of the new features in 10.2 | ||
| + | |||
* Easier <b>zoom</b>, perspectiveDepth on or off switching | * Easier <b>zoom</b>, perspectiveDepth on or off switching | ||
* 'hbonds on' does not calculate hbonds anymore. Instead, use '<b>hbonds calculate</b>'. This enables the separation of hbonds data present in the pdb file (e.g. calculated by a separate algorithm) and hbond information as calculated by the jmol hbond algorithm. | * 'hbonds on' does not calculate hbonds anymore. Instead, use '<b>hbonds calculate</b>'. This enables the separation of hbonds data present in the pdb file (e.g. calculated by a separate algorithm) and hbond information as calculated by the jmol hbond algorithm. | ||
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* The <b>stars</b> command creates better visibility of selected atoms. | * The <b>stars</b> command creates better visibility of selected atoms. | ||
| − | [http:// | + | |
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| + | == New in versions older than 10.2 == | ||
| + | Check the main Jmol website for the [http://jmol.sourceforge.net/history/index.en.html#History%20of%20Changes changelog] of the older versions. | ||
Revision as of 16:43, 8 June 2007
- Description of files in Jmol+JSmol distribution
- File formats read or written by Jmol
- The Jmol scripting interface
- Scripting as a programming language
- Complete reference of scripting commands:
- Loading models directly from databases
- Mouse manual
- Default colors used by Jmol
- Atom sets predefined in Jmol
- Support for bond orders · isotopes · stereochemistry · hydrogen bonds
- Jmol as editor
- Multi-touch support
- Copying and pasting state scripts between applets.
- Backward compatibility (changes of behavior across versions)
- Features added since version 10
- Users mailing list (and a mirror)
New in version 10.2
click here for interactive examples of the new features in 10.2
- Easier zoom, perspectiveDepth on or off switching
- 'hbonds on' does not calculate hbonds anymore. Instead, use 'hbonds calculate'. This enables the separation of hbonds data present in the pdb file (e.g. calculated by a separate algorithm) and hbond information as calculated by the jmol hbond algorithm.
- extended label formatting options, printing three-letter, one-letter amino acid codes possible, also including all available atom information (e.g. coordinates) in the label.
- the pop-up menu when right-clicking the applet can be disabled with 'set disablePopupMenu TRUE'. The pop-up menu itteself also can be tweaked.
- An advanced selection option based on connectivity is introduced: select connected It can for example select based on the amount of connections an atom has, or to which atom it is connected.
- Default atomype coloring within a running applet can be changed by e.g. 'color hydrogen yellow'. Coloring of specific selections overrides the default coloring, as before.
- Complete control of drawing bonds between (selected) atoms is now possible with the 'connect' command. Drawing of h-bond, double, triple, aromatic bonds is possible.
- orbitals and electron density and other information can now be drawn as isosurface or pmesh.
- advanced polyhedra bonds are introduced.
- The stars command creates better visibility of selected atoms.
New in versions older than 10.2
Check the main Jmol website for the changelog of the older versions.
