Jmol

Jmol 11.1 prelease development versions for Jmol 11.2 are in active late-stage beta testing. We encourage developers interested in the broader range of capabilities listed below to try Jmol 11.1. Jmol 11.1 represents a revolutionary new way to work ... [More] with and visualize molecular data. A new navigation mode for Jmol 11.1 allows scripted or unscripted "fly-throughs" of the model. Fasten your seat belt and take a ride on a protein's backbone from one end to the other. Jmol 11.1 introduces a whole new vocabulary of scripting. Fully backward-compatible with Chime and RasMol, Jmol scripts now allow for a broad range of user-defined data types and selective application of external file atomic data to a model for color-based visualization of properties. Variables can be defined and manipulated using a simple arithmetic involving boolean (true/false), integer, decimal, string, array, point, and plane data types. Jmol 11.1 introduces full support for multiple file loading, with the option of multiple models within the various loaded files. Files can be loaded sequentially into new "frames" or appended into the current frame so as to merge two datasets into one. Jmol 11.1 supports translation, rotation, spinning, and point/plane inversion of selected atoms, allowing a completely new way of working with a model. Jmol 11.1 introduces industry-standard translucency of objects, producing vivid rendering of multiple translucent objects at eight levels of translucency. Jmol 11.1 allows on-the-fly creation of variable-scale JPEG "snapshots" of the displayed window both by the application and the applet. Scripted writing of these snapshots allows creation of AVI movies using commonly available tools such as Microsoft Movie Maker. Jmol state "snapshots" can now be used to clone a model from the applet or application in order to view it in a pop-up window, save it for later retrieval, send a specific view of a specific model via email to a colleague. Additional new features of Jmol 11.1 can be found at http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm [Less]

Jmol 11.1 prelease development versions for Jmol 11.2 are in active late-stage beta testing. We encourage developers interested in the broader range of capabilities listed below to try Jmol 11.1. Jmol 11.1 represents a revolutionary new way to work with and visualize molecular data. (0 comments)

Jmol 11.1 prelease development versions for Jmol 11.2 are in active late-stage beta testing. We encourage developers interested in the broader range of capabilities listed below to try Jmol 11.1. Jmol 11.1 represents a revolutionary new way to work with and visualize molecular data. (0 comments)

Jmol 11.0 introduces a revolutionary way of delivering molecular surfaces over the web -- the Jmol Voxel File Format (JVXL). With a compression ratio on the order of 300-600:1 over color-mapped CUBE files, the JVXL format allows delivery of full ... [More] protein color-mapped solvent-accessible and solvent-excluded surfaces in 30-60 Kb instead of 10-20 Mb, making practical delivery of molecular surfaces available on the web for the first time ever. The Jmol application can write these surface files to disk. After transferring the JVXL file to a web-site directory, applets at that site can display the surfaces almost instantly. Command line options for the application allow surfaces to be created automatically if desired. Supported surface types in Jmol 11.1 development versions include: fixed-atomic-radius surfaces adjustable-radius van der Waals surfaces solvent-accessible surfaces solvent-excluded surfaces biomolecular cavities molecular orbitals molecular electrostatic potential maps color-contour-mapped planes arbitrary f(x,y) surfaces color-contour-mapped arbitrary f(x,y) surfaces Details relating to the JVXL file format can be found at http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf with numerous illustrated examples at http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/isosurface.htm and http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm [Less]

Jmol 11.0 introduces a revolutionary way of delivering molecular surfaces over the web -- the Jmol Voxel File Format (JVXL). With a compression ratio on the order of 300-600:1 over color-mapped CUBE files, the JVXL format allows delivery of full ... [More] protein color-mapped solvent-accessible and solvent-excluded surfaces in 30-60 Kb instead of 10-20 Mb, making practical delivery of molecular surfaces available on the web for the first time ever. (0 comments) [Less]

Jmol 11.0 introduces a revolutionary way of delivering molecular surfaces over the web -- the Jmol Voxel File Format (JVXL). With a compression ratio on the order of 300-600:1 over color-mapped CUBE files, the JVXL format allows delivery of full ... [More] protein color-mapped solvent-accessible and solvent-excluded surfaces in 30-60 Kb instead of 10-20 Mb, making practical delivery of molecular surfaces available on the web for the first time ever. (0 comments) [Less]

Jmol 11.0 introduces a revolutionary way of delivering molecular surfaces over the web -- the Jmol Voxel File Format (JVXL). With a compression ratio on the order of 300-600:1 over color-mapped CUBE files, the JVXL format allows delivery of full ... [More] protein color-mapped solvent-accessible and solvent-excluded surfaces in 30-60 Kb instead of 10-20 Mb, making practical delivery of molecular surfaces available on the web for the first time ever. The Jmol application can write these surface files to disk. After transferring the JVXL file to a web-site directory, applets at that site can display the surfaces almost instantly. Command line options for the application allow surfaces to be created automatically if desired. Supported surface types in Jmol 11.1 development versions include: fixed-atomic-radius surfaces adjustable-radius van der Waals surfaces solvent-accessible surfaces solvent-excluded surfaces biomolecular cavities molecular orbitals molecular electrostatic potential maps color-contour-mapped planes arbitrary f(x,y) surfaces color-contour-mapped arbitrary f(x,y) surfaces Details relating to the JVXL file format can be found at http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf with numerous illustrated examples at http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/isosurface.htm and http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm [Less]

We recommend that all developers of new web pages utilizing Jmol upgrade to Jmol 11.0 if currently using Jmol 10.2. (0 comments)

We recommend that all developers of new web pages utilizing Jmol upgrade to Jmol 11.0 if currently using Jmol 10.2. (0 comments)

After a long period of only development releases, the first stable release after 10.0 is out now. Many bugfixes and new features. (0 comments)