somewhere down below is the div with the applet
when it has loaded, click here:
testmac
this will start an animation with animation and spinning.
testmactestmactestmac
# With Jmol 11.7.33, you can visualize NBOs using Gaussian and the " $NBO AONBO=P $END" option. As for GAMESS, by default ALL MOs are read -- standard and NBOs. By excluding standard MOs with the FILTER "NBO" option to the load command, you can specify to only read NBOs. The filter "!NBO" selects all except NBOs.
# With Jmol 11.7.32, you can visualize NBOs using GAMESS and the " $NBO AONBO=P $END" option. By default ALL MOs are read -- standard and NBOs. By excluding standard MOs with the FILTER "NBO" option to the load command, you can specify to only read NBOs. The filter "!NBO" selects all except NBOs.
# Jmol 11.7.31 introduces a way to align structures across a set of frames. This is important for certain animations. The atom expression is evaluated per frame, and the resultant point is aligned in each case.
# Jmol 11.7.31 can read and display molecular orbitals for more than one model. Molecular orbitals are created for all visible frames. Animation then displays these orbitals as the frames change.
35. autoLoadOrientation and restore orientation DEFAULT
# Jmol 11.7.30 saves the view of Spartan and Sygress (CAChe) files and can restore that view automatically at load time (set autoLoadOrienation TRUE) or later at any time (restore orientation DEFAULT). Try loading these files with and without these options.
# Jmol 11.7.27 adds the capability to read surfaces of the Wavefront OBJ type. Only the vertex, group, and face records are used. The group records define sets of faces that can be loaded selectively using an integer after the filename. In addition, if the group name is of the form "g kRRGGBB", then RRGGBB is interpreted as a hexidecimal color key. The generated isosurface may be saved as a JVXL file using a new extension of that format that allows compression of face-color data. The surfaces may also be mapped or recolored in a solid color as can any other surface. Future versions of Jmol may utilize the Material (.mtl) file associated with these objects to better specify color.
32. isosurface CONTOUR and CONTOURLINES|NOCONTOURLINES
# Jmol 11.7.27 adds contour lines for mapped data. Hovering over these lines displays the value of the mapped function at this point. The default is 10 contour lines.
# Jmol 11.7.26 can calculate the area and volume associated with an isosurface. Values are reported and also stored in the variables isosurfaceArea and isosurfaceVolume, respectively. This measures the isosurface, not the model; whether or not this represents a good measure of the true molecular volume or area is unknown.
# Using set dragSelected in Jmol 11.7.25 you can move selected atoms around, translating them with ALT-SHIFT-LEFT mouse and rotating them around their geometric center using ALT-LEFT or CTRL-ALT-RIGHT. Selection halos are automatically turned on during mouse-drag actions. (Still a few bugs there....)
# Jmol 11.7.25 adds a new feature: You can type directly into the applet as though it were a console. To enable entry, start with CTRL-K or set allowKeyStrokes !allowKeyStrokes;set showKeyStrokes TRUE. Keystrokes are sent to the _KEYSTROKES echo, which is in the bottom left position. disablePopupMenu also functions to disable direct keyboard entry. A second CTRL-K disables keystrokes ( equivalent to set allowKeystrokes FALSE. CTRL-ALT-K can also turns keyboard entry of commands on and off, but not with display (set allowKeystrokes !allowKeystrokes;set showKeystrokes FALSE). When typing is enabled, the Jmol frank in the bottom right-hand corner will change color to blue (unsigned applet) or orange (signed applet).
# Jmol 11.7.23 adds the "-1" option to unit cell loading. This option forces full packing of the unit cell, which in some cases may be preferable to the 0 (unnormalized) or 1 (normalized) options. The common option to pack a single unit cell, {555 555 -1}, may be indicated using the PACKED keyword.
# Jmol 11.7.22 allows translation by absolute or percentage amounts in the x, y, and z direction. Distances may be in nanometers or angstroms and are measured in the plane parallel to the screen and going through the geometric center of the model. For Z, the zoom is adjusted such that the viewable portion of the model in that plane is increased by the indicated distance; a too-positive number for Z translation (making the dimension upon which zoom is based less than 1 Angstrom across) will be ignored.
25. error message returned in JavaScript inline loading methods
# A new Jmol.js file associated with Jmol 11.7.16 returns file loading error messages with jmolLoadInline, jmolLoadInlineArray, jmolLoadInlineScript, jmolAppendInlineScript, and jmolAppendInlineArray.
# Jmol 11.7.16 allows filtering of molecular orbitals in GAMESS files, where there may be more than one type. The filter uses ! as NOT and simply looks for lead-in lines that include or exclude the specified words separated by whitespace, commas, or semicolons. With NOT, the words are ANDed:!optimized,natural -- not optimized and not natural; otherwise they are ORed: initial,natural -- initial or natural.
23. Out Of Memory Error handling and jmolGetPropertyAsString("errorMessage")
# Jmol 11.7.16 traps out-of-memory errors along with other compilation and scripting errors and saves the message in a property that can be checked. In this example we attempt to load a huge biomolecule that with previous versions of Jmol would crash the applet. After getting an error, click here. Still, it is possible to lose the applet or LiveConnect if this is done multiple times.
# Jmol 11.7.14 adds the capability to flush saved information from memory. All of the save command options may be deleted, including bonds, coordinates, orientation, selected, state, and structure.
# Jmol 11.7.13 introduces the capability to split the left and right eye images for stereo rendering into two different applets. This may be useful when the stereo image is to be displayed using a single monitor split between two cross-polarized projectors using the method of GeoWall. The command to initiate this is simply sync * stereo or sync "X" stereo, where X is the extension of an applet -- 0 for "JmolApplet0". All scripting and control is then carried out on the applet for which the command was issued (generally the applet on the left). The right-eye stereo image is then sent directly to the right-side applets's Graphics object. See syncstereo.htm.
# Jmol 11.7.12 adds efvet (ef-site.hgc.jp/eF-site) surface file reading. These surface files contain vertex and triangle information but no "cube data". They are more similar therefore to pmesh files than isosurface files. However, they are particularly useful because they contain mapped data property information. This information is accessible using an integer after the filename. An XML comment in these files may identify the order of properties. In the example given here, the order is: (1) electrostatic_potential, (2) hydrophobicity, (3) temperature_factor, (4) minimum_curvature, and (5) maximum_curvature. In order to accomodate this type of file, a new JVXL file format was required. While Jmol 11.7.12 will still read JVXL 1.0 files, the new JVXL 2.0 files produced from vertex/triangle-only formats (pmesh and efvet) cannot be read by previous versions of Jmol.
# Jmol 11.7.12 deprecates the PMESH command. This functionality has been merged with ISOSURFACE. You can still use the PMESH command, but it executes the ISOSURFACE command the same as any other ISOSURFACE command except for one property: files containing pure numbers are assumed to be pmesh files rather than cube files. The keyword PMESH can be added to any isosurface command to indicate that the next file read is in PMESH data format.
# Starting with Jmol 11.7.11, both MESSAGE and comments starting with # can act as the target of a GOTO command.
15. set hbondsAngleMinimum, set hbondsDistanceMaximum, and calculate hbonds {atomset1} {atomset2}
# Jmol 11.7.9 includes the option to calculate hydrogen bonds betweens any set of pairs of oxygen or nitrogen atoms that do not have H atoms attached. hbondsDistanceMaximum sets a maximum distance in Angstroms between the two heavy atoms (default 3.25). hbondsAngleMinimum (default 90) sets a minimum angle between the two heavy atoms and any atom attached to one or the other of those atoms. Note that some thought might be given to which oxygens are to be connected. The default will connect carbonyl groups. It is important to understand that these calculated hydrogen bonds are only where hydrogen bonds might be, not necessarily where hydrogen bonds actually exist.
# Jmol 11.7.8 allows renaming of atoms. If an array is specified, then the elements of the array are matched sequentially to atoms until the array or the list of atoms is exhausted. White-space characters should not be used in these names.
# Jmol 11.7.8 adds the option to select atoms based on atom names using the within function. The search is case-sensitive. While in general atoms can be selected just using their name -- select C3 -- this method allows for both a more specific and a more generally applicable atom name search option.
# Jmol 11.7.8 allows setting the atom type of an atom. If an array is specified, then the elements of the array are matched sequentially to atoms until the array or the list of atoms is exhausted. White-space characters should not be used in these types.
# Jmol 11.7.8 adds the option to select and display atom types for mol2 and AMBER topology files. For other file types, type simply refers to the atom name (which is effectively an atom type in PDB files, for instance). Note that selection IS case sensitive. (NOTE: 11.7.2 was released with "type" instead of "atomType". 11.7.8 allows now just for "atomType".
# Jmol 11.7.8 allows dynamic assignment of an element to an atom. The atom color is automatically changed back to its CPK default color. Either the atomic number or the element symbol can be specified.
# Jmol 11.7.3/11.7.10 adds the cd command to display and set the default directory. With the signed applet or application, this can be either a local or web-based path. No comments are allowed on the CD line unless the path is in quotation marks. The CD command also sets the defaultDirectoryWrite parameter, which independently from the defaultDirectory parameter sets the directory used for the application and signed applet write command.
# The Jmol 11.7.3 file() function returns the full path to the specified file. If the filename contains a question mark and the applet is signed, a file dialog is displayed that allows the user to change directories (Jmol 11.7.3). Note that load("filename") returns the file contents of the file, not just its path. If the file is the empty string, the result is the current directory.
# Jmol 11.7.3 introduces load MODELS and expands load TRAJECTORY with the option to do so as an APPEND operation. Two syntaxes are allowed. MODELS/TRAJECTORY {first,last,stride} (commas optional) loads selected models of a set from a first model to a last model, with a step of stride. These numbers are zero-based and refer to the index of the model in the file (not the PDB MODEL record number associated with a model). A -1 for last indicates "to the end of the file." A second syntax allows selection of any set of models in a collection. This syntax uses the Jmol "bitset" notation involving parentheses, braces, ranges of values using colons, and no commas.
# Jmol 11.7.1 allows reading of AMBER molecular dynamics topology and coordinate files. The command allows for one topology file and any number of coordinate files to be specified. One of the keywords FILES or APPEND is required, and at least one COORD keyword must be present. FILES replaces any current models with the trajectory; APPEND (starting with Jmol 11.7.3) creates a separate trajectory that can be overlayed with another using, for example, frame *;display 1.1,2.1. Any number of {first,last,stride} may be present. If multiple {first,last,stride} are present, each must be preceded by a new COORD keyword. If {first,last,stride} is not present, {0,0,1} is presumed -- that is, ONE trajectory step from each file. A -1 for last indicates "to the end of the file." The FILTER keyword is strongly recommended. In particular, "![WAT]" is recommended so as to not load water atoms, thus saving memory. The prefix "mdcrd::" is required on AMBER coordinate files, since those files have no header to distinguish them, and Jmol does not use file extensions for file typing. All file names must be quoted. Coordinate data are loaded as Jmol trajectories. This means that there is one set of atoms, and when a frame change is made, only the coordinates change. It is possible to superimpose multiple trajectory steps, but in order to do that one must load the fileset multiple times, using load FILES for the first trajectory and APPEND for the others. Jmol 11.7.3 adds the capability to load any specific trajectory steps using the bitset notation ({a b c:d e})