Difference between revisions of "Features since version 10"
Jump to navigation
Jump to search
Jmol + JSmol Documentation
AngelHerraez (talk | contribs) m |
AngelHerraez (talk | contribs) m |
||
| Line 6: | Line 6: | ||
== New in version 10.2 == | == New in version 10.2 == | ||
| − | [http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-10.2/new.htm | + | [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 | + | * '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. |
| − | * | + | * Extended <b>label formatting options</b>, printing three-letter, one-letter amino acid codes possible, also including all available atom information (e.g. coordinates) in the label. |
| − | * | + | * The <b>pop-up</b> 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: <b>select connected</b> It can for example select based on the amount of connections an atom has, or to which atom it is connected. | * An advanced selection option based on connectivity is introduced: <b>select connected</b> It can for example select based on the amount of connections an atom has, or to which atom it is connected. | ||
| − | * <b>Default | + | * <b>Default atomtype coloring</b> 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 <b>drawing bonds</b> between (selected) atoms is now possible with the 'connect' command. Drawing of | + | * Complete control of <b>drawing bonds</b> between (selected) atoms is now possible with the 'connect' command. Drawing of hydrogen bonds, double, triple, aromatic bonds is possible. |
| − | * | + | * Orbitals and electron density and other information can now be drawn as <b>isosurface</b> or <b>pmesh</b>. |
| − | * | + | * Advanced <b>polyhedra</b> bonds are introduced. |
* The <b>stars</b> command creates better visibility of selected atoms. | * The <b>stars</b> command creates better visibility of selected atoms. | ||
Revision as of 11:20, 9 October 2008
- 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)
A more recent list of changes is compiled in SorceForge project pages, and listed and linked from the Jmol website: www.jmol.org/history/ (see 'History of Changes' section there).
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 atomtype 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 hydrogen bonds, 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.
