Click on a link below to see what it does. You can also type a command in the box below the model to see its effect. The script run in this case was ;set echo top left;echo loading quartz.cif...;delay 1;load "quartz.cif" {1 1 1};message done.
This page lists all new features introduced between Jmol 10.2 and Jmol 11.0. Other files list features introduced between Jmol 11.0 and Jmol 11.2 and planned for Jmol 11.4. Documentation is also available. There is also a simple list of script modifications. Take a look and see what is new. Comments? Suggestions? Bob Hanson
Jmol 10.9.104 introduces set scriptDelay n where n is a number of seconds to delay prior to execution of each script command. This is primarily for debugging/demo purposes.
Jmol 10.9.103 introduces initialize, which resets all parameters to default values and clears the model using zap.
117. jmolLoadInline([line1, line2, ....]) for array data types
Jmol 10.9.103 introduces the capability to load inline an array of data rather than a long string. Basically, an array of lines can now replace a single string. Because this form involves no new-line characters, it is distinguishable within Jmol from the syntactically identical function that loads multiple models.(topic 107) and for more recent modifications to this functionality Jmol 11.4 topic 69
Jmol 10.9.99 introduces the capability to load multiple models of multiple types using the data command. Simply define a separator and then use that separator between models.
Jmol 10.9.98/99 introduce a FULL implementation of the capability to create a "serialized snapshot" of the state of the applet or application. This snapshot is in the form of a set of Jmol script commands. These commands reproduce the exact state of Jmol in existence when they were generated. Implemented in 10.9.98: atoms, bonds, labels, echos, cartoons, draw, halos, meshRibbons, ribbons, rockets, stars, strands, trace, nondefault settings, orientation, spinning, zoom; 10.9.99 adds all remaining shapes (dipoles, dots, geosurface, isosurfaces, lcaoCartoons, molecular orbitals, and vectors), vibration, and animation. run (just about) any command on this page, save the state, run some totally different commands, then restore the state. Note that isosurfaces will not be reproduced
Jmol 10.9.98 allows for atom-specific "label pointers" -- lines that connect labels to their respective atoms. These lines are color-keyed either to the text color (set labelPointer on) or the background color, if a background is shown (set labelPointer background).
Jmol 10.9.97 introduces a new command, subset, which defines a set of atoms. subset limits all further atom expressions in ANY command to act only within this subset. It does not actually select anything by itself, however. In action, it appends "AND subset" to whatever is being indicated in any command that uses atom expressions (measure, for example). So, for example,
By itself, this may not seem that useful, because you could just select that set anyway. In some ways it is just a convenience, allowing the command set to be applied to different subsets. Select one of the following subsets, then apply one of the restrict commands
Note that since all user-clicks and menu action works though the command processor, setting a subset also affects user action. For example, subset provides a way of making sure that anything done by the user (via the menu) or subsequent button pushes operates only within a certain set:
Jmol 10.9.95 adds set sheetSmoothing. In conjunction with set TraceAlpha, a value of 1 here tells Jmol to use midpoints (like Rasmol) rather than alpha carbons for the sheet segments only. Default in 10.9.96 is set to set traceAlpha on; set sheetSmoothing 1;
111. set hermiteLevel and smoother cartoons; set highResolution
Jmol 10.9.93/94/95 introduce a more sophisticated look for cartoons and other secondary structure depictions. The smoothness level of the Hermite curves can be increased or decreased using set hermiteLevel n where n is -8 to 8. The default is 0 (10.9.96) giving 10.2-like flat ribbons and rough rope-like traces. A value of 4 or -4 might be a good starting choice. Positive values revert to 0 when the model is in motion; negative values continue the smoother rendition even when the model is being manipulated. A word of caution: Setting the hermite level to -8 can significantly slow processing during moveTo commands. Higher positive or negative numbers may result in out-of-memory conditions for very large models. Generally Jmol will not use a mesh if the screen size of the object is relatively small. You can force Jmol to use mesh-based rendering even when the structures are small with set highResolution.
Jmol 10.9.92 introduces set ribbonAspectRatio for adjusting the thickness of the ribbons in both cartoons and ribbons. 0 turns this feature off; 8 to 20 probably advisable. Higher numbers lead to thinner ribbons. The set traceAlpha option directs Jmol to create a trace (which is also the basis for ribbons, strands, and cartoons) directly through the alpha carbons rather than through their adjacent midpoints.
Previously, only a few file types included atom names. Now all atoms from any file type are assigned an atom name (which appears upon hovering on an atom and also in the atom label and in message and pick callbacks). Atoms can now be selected based on this atom name.
The common wildcard asterisk * can now be used in PDB group names and NON-PDB atom names. (Not PDB atom names, because some PDB atom names include "*", such as "O5*" in DNA.
107. jmolLoadInline([model1, model2, model3,...]) for multiple file types
Jmol 10.9.86 introduces the capability to load inline multiple files of different type. Basically, an array of model strings can now replace the single model string in jmolLoadInline() and jmolLoadInlineScript(). See also topic 117and for more recent modifications to this functionality Jmol 11.4 topic 68.
Jmol 10.9.85 introduces a simple idea: allow echos to be anywhere is model space, not just on the surface of the window. It is as simple as indicating a coordinate or an atom expression.
Jmol 10.9.85 allows for adjusting the zoom either by the smaller dimension of height and width (set zoomLarge false) or the larger one (set zoomLarge true, the default). You will not see an effect here, because this window is square.
Jmol 10.9.79 adds rudimentary if;else;endif capability using the "set" options. Click this next link twice. IF commands can be nested up to 10 deep. The syntax is minimal; only one test is allowed, optionally preceded by NOT, as in "if (NOT showBoundBox);...;endif;"
Jmol 10.9.79 adds a new pop-up menu that is accessed by clicking on the Jmol frank. This menu is a quick route to any submenu that you have recently accessed. Try coloring something using the pop-up menu. Now color it another color. Notice how long it take to find the right menu the second time. Now click on the frank and see that your menu is just a mouse jiggle away.
Jmol 10.9.77 adds the capability to load a wider range of unit cell blocks. The range should include 555 (the base unit cell). The third parameter, 0 or 1, indicates whether(1) or not(0) to "normalize" the symmetry operations by moving the geometric center of the generated set of atoms back into unit cell 555.
Jmol 10.9.76 adds two new commands, hide and display, and two new selectable terms, hidden and displayed. They are exact opposites of each other, provided for convenience only. display is similar to restrict except it is fully reversible. Like restrict, display hides unselected atoms, but unlike restrict, you can display all later and see everything come back as it was before.
Jmol 10.9.71 allows you to select the currently clickable atoms. In conjunction with slabbing, this means that you can now select for just those atoms that are within the depth/slab range. A later slab off; restrict selected now allows you to manipulate the model with that particular slab maintained. Be sure to do a refresh just before selecting.
93. slices through a molecular surface and new way to define plane
Jmol uses a unique algorithm to calculate surfaces. Each position in space is given a value that is its distance from the nearest surface point. What this means is that a "surface" is really an "isosurface with cutoff 0". And what that means is that a surface is no different in terms of visualization from a molecular orbital or other atom-based spacial property. Jmol 10.9.71 allows you to generate slices through a surface.
generated from the following command (which takes several seconds on my machine). Note the new way to define a plane simply in terms of three points -- (atom)s or {coordinate}s
Jmol 10.9.72 introduces the "hkl" keyword indicates that the next three numbers in braces are Miller indices. Note that all coordinates are implicitly fractional. A faster alternative is to use "solvent 0" instead of "molecular".
Jmol 10.9.71/79 allows you to select the exact lattice translation for a given symmetry operation. The reference point is the untransformed, untranslated file atoms - Jones-Faithful x,y,z - which are always designated n555.
Note that you can use other comparisons -- !=, <, >, <=, and >=. If you use any of these comparisons with a simple symmetry operation, the usual comparison will be returned. If you use this new nijk syntax, then the atom must match the given symmetry operation; the comparison is ONLY for the ijk part.
Jmol 10.9.68 lets you do quite a bit with no model. Echo, draw, isosurface, pmesh, dipole, rotate, spin, zoom -- all these are operational before ever loading a model and also after zap. Maybe there IS a use for zap!
Jmol 10.9.68 adds the capability to read the system clipboard in the application with a new Edit...Paste menu item. For the applet, that is not possible without signing, so instead open a console, paste your clipped data into the lower (input) box, and press Load.
Jmol 10.9.63 allows saving and restoring of the current selection set. Basically this is a "global define" that crosses the load barrier. Used without "load" between save and restore, the action is the same as define xxx selected...select xxx. The difference is that the file can be reloaded between save and restore.
Jmol 10.9.63 simplifies the selectionHalo business by introducing the selectionHalos command. It's the equivalent of "set showSelections" or "set display selected" but it's simpler and corresponds better with the color selectionHalos command.
Jmol 10.9.63 introduces isosurface MEP, with which you can display molecular electrostatic potentials. These potentials are calculated from partial charge data present in a file; Jmol cannot calculate these charges. Just the MEP:
With Jmol 10.9.63 you can use the pop-up menu item "show" to show all sorts of information about the model. This information pops up in a console window that appears in front of the web page. This can be done in script as well, using the "console" command.
Jmol 10.9.62 allows you to set the default font, color, background, and alignment for echo text using "set echo none". Also, for echo, anytime you set a characteristic, that characteristic becomes the new default value.
Jmol 10.9.62 adds the convenience the capability of designating a color and/or TRANSLUCENT/OPAQUE when generating polyhedra. No need for an additional "color polyhedra ..." command, though that is still present.
Up until this point, Jmol either always used the secondary structure defined in a PDF or mmCIF file or calculated it itself only when the file was loaded. This is a problem for some models where only a portion of the bonding is indicated in the file. Jmol 10.9.62 adds the capability to recalculate this secondary structure anytime, but particularly after using the connect command to fill out the bonding.
Jmol 10.9.61 adds isotope support for deuterium and tritium. Element symbols "D" and "T" are recognized, and you can "select deuterium" or "select tritium". Note that when you "select hydrogen" you get any isotope of hydrogen. Suggestions for colors are welcome. Standard file formats should be supported, including CIF, PDB, MOL, and XYZ.
Jmol 10.9.61 adds set forceAutoBond which forces Jmol to ignore bonding indicated in a file and apply its own bonding rules. This is useful in cases where, for example, a PDB file has only some of the connections indicated, which otherwise would create gaps in the secondary structure and missing bonds.
Jmol 10.9.60 adds save bonds and save orientation. Any unique identifier or number can be used to identify the save/restore set. If no name is given for restore, then the last saved item of the given type is restored. For restoring orientations, a parameter can be added that indicates the number of seconds over which the reorientation should take place. More to come!
Jmol 10.9.60 adds an important isosurface option: ignore. The idea is to completely ignore a given set of atoms, most likely solvent. (Note: 10.9.74 makes "ignore(solvent)" the default option for "solvent" and "sasurface"). For a model that contains water or other solvent, it is quite possible that we want a surface that ignores these parts. Adding ignore(solvent) tells Jmol to completely ignore these atoms for the purposes of calculation. This option must be indicated BEFORE the sasurface or solvent parameter, because it is used in the construction of the surface.
Jmol 10.9.60 adds the capability to define a single static model that remains present during an animation or, for that matter, any situation when more than one model or frame is present (as in multiple-file loads). This option has limitations and is not recommended when setting display properties.
Jmol 10.9.60 introduces the capability to visualize based on distance from the molecular surface. The distance calculated is well defined. 0 means "on the surface"; all other distances are the minimum distance of an atom to one of the surface atoms.
Jmol 10.9.60 introduces a new "calculate" command that currently has two arguments -- "surface" and "hbonds" (same as "hbonds calculate"; the idea here is that there may be other quantities to calculate in the future). This does no rendering, just the calculation. superceded in Jmol 11.4 by calculate surfaceDistance [within|from]
Jmol 10.9.59 introduces the "halo" object, similar to in action to "stars" but a ring instead of a cross. These are the "selection halos" generalized, colorable, and sizable. Jmol 10.9.63 introduces the selectionHalos command. Halos have a different default color setting if generated using "halos on" (color of the atom) or "select *;selectionHalos ON". In the latter case, the color is the "selectionHalos" color, originally gold, but settable using "color selectionhalos xxxx".
Jmol 10.9.58 adds an infinite number of independent echo placements. Simply provide a unique name followed by the x and y positions for the label. "0 0" is the bottom left corner.
The old "top", "middle", and "bottom" are simply special pre-defined locations. In these three special cases only, "left", "right", and "center" describe both the window placement and the text alignment.
Jmol 10.9.55 extends spacegroup and unitcell capabilities to standard XYZ, mmCIF, and MOL files. Coordinates are not fractional in these files, so the presumption is that we have the final Cartesian coordinates, but we want to "reverse engineer" the system and see how that molecule packs in its crystal. For this we have to have some additional information of spacegroup and unitcell.
Jmol 10.9.54 adds the capability to explore space groups and molecular packing of proteins in PDB files. This opens the door also for the same using any Cartesian-coordinate file, provided unit cell and space group information are provided. At least for now it is possible with PDB files.
Jmol 10.9.53 introduces set labelsGroup, which places the labels for atoms in proteins and nucleic acids just in front of their group, rather than in front of all atoms, as in set labelFront.
Jmol 10.9.52 introduces a general method of entering data into Jmol, mostly for future customizability options. The one option currently supported is "model" data, but any sort of line-based data can be introduced and later shown using the show data or getProperty dataInfo commands. The data "model" statement allows in-line entry of a file surrounded by additional script commands. See the documentation for details and an example.
To select all special positions (positions that can be generated by more than one symmetry operation from the original set of atoms), use select specialPosition.
Jmol 10.9.51 adds the capability to read space group names (Hermann-Mauguin or Hall) and from these to generate the set of operators. In the case of Hall symbols, this assignment is definitive; in the case of Hermann-Mauguin symbols, cell parameters are also used in order to identify the unique axis, but there still may be ambiguities in this case. The current implementation is for testing only -- some changes should be expected. To indicate 2", use a pair of single quotes: 2''. In addition, you can supply a desired space group name with a file to specify that you want to override the space group indicated in the CIF file.
without qualifiers, "show spacegroup" interprets the name of the spacegroup given in the file. Note that this may not be consistent with the operators used to calculate the atom positions if those are explicitly given in the CIF or RES file. Jmol will only use the space group name to generate operators if they are not otherwise given in the file.
In 10.9.52 you can load a file and script what spacegroup to use, overriding the spacegroup indicated in the file itself. No check is done to ensure that the chosen space group is compatible with the cell dimensions. The "space group" can just be a list of x,y,z operators.
in response to several users' request, dots now functions on the selected atom set without turning off other dots. In addition, there are now two options, set dotSurface TRUE|FALSE and set dotsSelectedOnly TRUE|FALSE. The first of these, set dotSurface (default TRUE) indicates that we are to draw the dots with neighbors in mind, not rendering dots that would be "inside" another atom. If you turn dotSurface OFF, then dots are just spheres of dots symmetrically positioned around the selected atoms. Turn them on or off just like labels. The second, set DotsSelectedOnly (default FALSE) indicates whether or not to draw the dots only for the atoms that are currently "dots on". The idea here is that sometimes we might want dots to show a fragment of a surface (set dotsSelectedOnly FALSE) or to show a smooth curve around all currently dotted atoms (set dotsSelectedOnly TRUE). To see any effect with either of these, you need to do another dots ON or other related command.
although Jmol uses the DSSP hydrogen bond calculation as described at http://en.wikipedia.org/wiki/Secondary_structure, there seems to be a flaw in this energy calculation that renders too many hydrogen bonds. I've added the criteria that the N--H hydrogen must be closer than the N--H nitrogen to the carbon of C=O for a valid hydrogen bond to be claimed, and also that the H--O distance of the hydrogen bond itself must be less than 3.0 Angstroms. (2.0 is probably more realistic, but 3.0 allows for some slop.) The result of this is that it is possible that slightly fewer (but more realistic) hydrogen bonds will be displayed for PDB and mmCIF files. Note that if a file contains no indication of hydrogen bonds, then one must issue a hbonds calculate command first before any hydrogen bonds will display.
10.x.46 introduces a means of customizing (or removing) the default listing of information that appears with a molecular orbital when using the MO command. See mo.htm
10.x.45 introduces dynamic setting of the default directory as well as the applet proxy server. Using set defaultDirectory "directoryName" you can change where files are coming from without moving the files all around. This should prove helpful to those of us who test pages on more than one server or hard drive.
Using set appletProxy "serverURL" you can set the URL that Jmol goes to in order to display files NOT from the applet's host. This requires specific code on the server side that takes a call such as "www.myserver.com?url=someother.server.com/myfile.xyz" and returns the file at someother.server.com/myfile.xyz.
When a special picking mode is set (distance, angle, or torsion), the pick callback continues to indicate the individual atoms picked; the message callback function gets the final information.
10.x.44 introduces set picking DRAW, which allows you to change the positions of the vertices that define points, lines, planes, arrows, and curves. The command show draw then delivers the command that can be used in web pages to reproduce this set of vertices.
10.x.42 tests an idea for displaying cartoons as rockets. The idea is to have a flag that can be set that renders cartoons in the form of rockets. The original rockets and cartoons are thus both still there.
note that the rendering of the turns is not precisely the same as either cartoons or rockets, because we have to connect to both ends of a rocket, which are not in the same place as the ends of an alpha helix, and we have to connect to both ends of a sheet, which are not in the same place as the rectangular rocket arrows. I am not fully satisfied with this rendering.
Jmol 10.x.40 adds select/restrict within(SITE,expression), select/restrict within(ELEMENT,expression), select/restrict site=n, and select/restrict element=n. (This last is just for completeness sake. "select elemno=n" already exists.) These options are of particular use in the context of crystallography, where symmetry may generate several atoms with the same site but different cell position.
This loads 3x3x3 = 27 unit cells. Note that without "and visible" all matching atoms are selected and that "and visible" should appear outside the "within()" phrase.
Jmol 10.x.40 adds set picking SITE and set picking ELEMENT. In each case, all atoms that match the specified site and element and are visible are selected.
Jmol 10.x.33 supports HoverCallback. When a user's mouse hovers over an atom, the function specified in jmolSetCallback("hovercallback","functionName") gets a call. The first parameter in the callback is the applet id. Second is a descriptive string indicating the atom's identity and xyz coordinates. Third is the atom's index (atomIndex), which can be used with
jmolGetPropertyAsArray("atomInfo")[atomIndex]
to get more detailed information if desired. Hovercallback is active even if hover OFF has been executed. Thus, with hover OFF the user will not see any effect of hovering, while the web page can be made fully aware of it. The call to jmolSetCallback() must be made BEFORE the call to jmolAppet().
Jmol.js supports Asynchronous JavaScript, allowing web developers to create pages that draw from any molecular data resource on the web. To use this service, nothing more than Jmol.js is require. No server-side application is needed. Currently the both of the two known AJAX-JS servers are supported -- one at St. Olaf College serving up RCSB biomolecular structures as well as just about any uncompressed structural model files anywhere on the web, and the American Mineralogical Society's AJAX mineral structure server at the University of Arizona.
Many people have reported issues with script commands running over each other. This problem is now largely solved. applet.jmolScript() and viewer.script() deliver scripts to a queue, and if that queue is turned on using set scriptQueue ON, they are properly sequenced. Thus, when the queue is turned on, each script waits for the previous to complete. This is NOT standard Jmol procedure for the reason that sometimes one needs one script to interrupt another, as, for example, when a LOOP command is involved. In that case, the only way to interrupt the looping script is with another script. So, to account for this issue, the roles of quit and exit have been expanded. quit or exit at the very beginning of a script command halts any previous still-running script and. Processing then continues with the second command on the line. Anywhere else in the command, quit and exit abort that script. In addition, exit clears the script queue of any remaining scripts, thus stopping all script processing. Try this with the following commands to see how it works. Go ahead and click rapidly to start more than one script with and without the script queue being on.
37. super-simple solvent-accessible surface option using "spacefill"; new variable radius dots and new geoSurface command
The "solvent-accessible surface" is defined as an extension of the van der Waals radius by a set "solvent probe radius", commonly 1.2 or 1.4 Angstroms. This surface is now displayable simply using the spacefill +1.2 command, where the +1.2 indicates "van der Waals radius plus 1.2 Angstroms
The same works for dots. The geoSurface object just involves connecting the dots. Probably not so useful with spacefill +12, but it was there already in the code, undocumented, so I have enabled it.
36. new select within("[SEQUENCE]",(atom expression))
Jmol 10.x.30 adds the capability to select specific atoms within a specific peptide or nucleic acid sequence. The one-character group codes are used to specify the desired sequence.
Jmol 10.x.29 adds the capability to draw LCAO "cartoon orbitals" at any hybridization-compatible atom very quickly without knowing anything about its orientation.
10.x.25 introduces a simple command that you can use to explore the molecular orbitals contained in a variety of file types. (New types added upon request.) The command allows for changing the cutoff value as well as the resolution of the surface, the colors, and the transparency. In addition, a plane can be specified, allowing for a slice through the orbital to be depicted.
33. Spartan .spartan file and Compound Document reader support
Wavefunction's Spartan native binary .spartan files can be read by Jmol starting with 10.x.22. These files are standard Compound Document file format (same as some versions of Microsoft Word and Excel, and OpenOffice files.) Jmol can read atoms, bonds, molecular orbitals, vibrational modes, charges, dipole moments, and a variety of other properties contained in these files.
Jmol 10.x.24 adds "set logLevel n" where n ranges from 0 (minimum of messages) to 5 (all messages). You can also use the JavaScript command jmolSetLogLevel(n) PRIOR to getApplet() to add a parameter to the code for the applet. For example, jmolSetLogLevel(0) will produce a SILENT applet.
Jmol 10.x.05 - 10.x.18 introduce VERY compact orbitals and other molecular properties as isosurfaces. These files are generated by Jmol from CUBE files with compression ratios on the order of 400 to 600:1 or from Jmol-generated data. High levels of compression are possible because JVXL files do not allow for variable cutoffs. check out the new "Jmol Voxel File" format at ch3cl.jvxl. For a discussion see JVXL-format.pdf
30. new "select/restrict cell={i j k}" and "unitcell {i j k}" and better polyhedral rendering
Jmol 10.x.18 allows for the selection of specific unit cells. Coordinates such as {1.5 1.5 1.5} are allowed. In conjunction with this, "unitcell {i j k}" shifts the unit cell and the unit cell axes ("set axesUnitcell") to a new origin. See poly.htm
Jmol 10.x.17 allows for the depiction of dipoles as arrows in space along the line of the bonds with which they are associated. Dipole vectors can also be placed between any two molecular coordinates, serving as generic arrows. The molecular dipole can be shown as well based on Spartan SMOL data. see dipole.htm
APPLET ONLY: "show url" with or without a filename in quotes after it, pops up a new window with that URL in it. If it begins with "http://" this URL can be from any server on the web.
Starting with Jmol 10.x.08, "set" is optional with axes, unitcell, or boundbox. note that true/false or on/off set commands now take "true" as the default Jmol 10.x.01 allows definition of the axes with respect to the external window frame, the molecular frame, or based on the unit cell. see draw.htm
In 10.2, "color measures" change all measurement colors at once. The change here is subtle. If measurement colors have already been set, then "color measures NONE" needs to be invoked to turn off measurement colors prior to resetting them. In addition, "color measurements" now acts on all future measures, allowing for selective coloring of measurements. Thus, "color measure" in 10.x acts on (a) any measures currently with no color assigned and (b) on any future measures. Note that there still is no selective RE-coloring of measurements.
a very narrow range of blue on chain A, because although only A has relevant values, and chain B variation is setting the range. no difference, because the color range includes chain B
19. points, lines, and planes; specifying coordinates
Jmol 10.x can now draw point, line, and triangular or rectangular planes based on single atom positions, group average positions, or specific molecular coordinates. see draw.htm
Jmol 10.x allows now for pmesh data to be give "in line" rather than from a file. This allows for simple definition of points, lines, and planes that is an alternative to the new "draw" command. see pmesh.htm
Jmol 10.x.03 introduces a way of specifying fractional coordinates: {1/2, 1/2, 1/2}. A "1" in the denominator is optional: {0.5/, 0.5/, 0.5/}, and in such cases only one slash is necessary: {0.5/, 0.5, 0.5} or {0.5, 0.5, 0.5/}. These may be used in defining the center, in creating draw objects, in defining rotation, spin, and moveto orientation axes, and positions of dipole moments. See fraction.htm
16. symmetry, unit cells, and multiple lattice reading
Jmol 10.x now allows extensive reading of SHELX and CIF symmetry and lattice information. Multiple unit cells can be displayed. see sym.htm and the Jmol Crystal Explorer
Jmol 10.x.13 allows for a much broader range of measurement calculation and display. All measurements fitting a certain minimum/maximum criterion and matching a specific set of atom selections can be displayed, and the data can be returned using the getProperty script command. see measure.htm
NOTE ONE COMPATIBILITY CHANGE: "measures OFF" does not delete measures; only hides them; "measures DELETE" added
Jmol 10.x.09 lets you set this flag so that when the user clicks on a set of atoms for a measurement, all such atoms in ALL models are measured. Works with scripted "measure" command as well. see measure.htm
Jmol 10.x expands the frame command to allow pausing and restarting from a specific frame, playing in reverse, and setting a specific range of frames within which to play. see measure.htm
Jmol 10.x allows for rotation and spinning around axes defined either internally with respect to molecular coordinates or externally (the standard way, using the window frame as a reference. see draw.htm
Jmol 10.x introduces the "molecule" selector, which selects all atoms covalently bonded to a specific atom or group of atoms. Whole molecules can then be colored or selectively highlighted. see the Jmol Crystal Explorer
Jmol 10.x now allows for multiple file loading. This in conjunction with conformations and alternative locations allows one set of file data to be loaded into two "models". Each model can be given a defined conformation, and then the two conformations can be displayed together. see altloc.htm
Jmol 10.x now allows embedded scripts in some data file types (XYZ, MOL, PDB). Not intended to be a replacement for scripts, this allows setting definitions or orientations or other such model-specific scripts so that they run any time the file is loaded. see pmesh.htm
Jmol 10.x.01 5/17/06 introduces "set defaultLoadScript" allowing the load command to execute a default script after successful file loading. see altloc.htm
2. reading Spartan smol data files, including vectors and all smol data into auxiliaryInfo
Jmol 10.x reads the entire set of data in Spartan SMOL files along with the coordinates and is available via "getProperty auxiliaryinfo". see spartan.htm
Jmol 10.x along with its associated new Jmol.js library now allows for the retrieval of a wide range of data related to the model. see vibrate.htm, and try the bracketed links, below:
