Tutorial on how to use the Jmol export to web function. Either you do not have Java applets enabled in your web browser or your browser is blocking this applet. Check the warning message from your browser and/or. Another choice is to save from Jmol both the model data and the current orientation, rendering, color, etc. For that, you use the pop-up menu and File > Export.
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Jmol will read any file and try to determine its format from its content. The file extension is not taken into account for identifying the format. You can instruct Jmol as to which format to assume using this special command syntax:.
Here is a list of format values. What follows is a collection of specifications and comments on several formats, but is not a complete listing of all formats supported. Feel free to add a subsection with a description of a format you know well. Contains atom coordinates and bonds. V the most common is limited to atoms.
Saving results from Jmol
These formats support formal charges and isotopes ; both are read by Jmol. The defining tag 2D or 3D must be located in line 2, columnsbut is ignored by Jmol, which just uses the Z coordinates provided, be they zero or not. Jmol reads Fxport files. Contains atom coordinates, bonds, substructure information. This format supports partial charges and isotopesbut only partial charges are currrently supported by Jmol.
A single MOL2 file may contain several structures, which will be read by Jmol as multiple models or frames. Contains atom coordinates and information on biomolecular residues, sequence, chains, hydrogen and disulfide bonds, secondary structure, biologically relevant sites, cofactors.
Can also contain temperature factor, formal charge, element symbol, alternate locations. This format supports formal charges, and only hydrogen isotopes as D and T ; they are all jjol by Jmol.
If you need support for partial charges, see the similar PQR format exporg.
Jmol can get files directly from the Protein Data Bank website. This format was originally from the XMol package, but has been widely adopted by many other programs. Contains only atom coordinates no bonds and, optionally, charges and vectors e. Supports multi-model data multi-frame, animations. An extension of this format supports isotopesand they are read by Jmol.
Example by Paul Bourke.
Details about the XYZ format. Jmol reads CIF files. Crystallographic Information File, the official format from the International Union of Crystallography:. Acta Crystallographica A CIF files may contain an inline script starting with jmolscript: Jmol can get files directly from the ligand collection at the Protein Data Bank website. Jmol reads ex;ort files. Macromolecular Crystallographic Information File, an expanded format to cope with macromolecules.
Jmol does not fully support reading of Alchemy and Alchemy files. A simple Alchemy reader is implemented starting Jmol Alchemy example and Alchemy description by Paul Bourke.
A complete specification of these formats would be needed to fully implement the reader. If you have those details, ex;ort contact the developers team.
Example files supported by Jmol. Jmol reads only the output format. Recent versions of Jmol application can also export to files in Gaussian input format. There jmoo example files of Gaussian input, output and log. Jmol reads Cube files, original from Gaussian software Gaussian website. Description of Cube Input and Cube Output formats: Description by Paul Bourke. Also, force vectors are read and included as vibrations activated by default on file load.
Description of the format. Example by Paul Bourke, and other example files. Details jml HIN format. Jmol reads and writes PQR files. Jmool, since they are very similar to pdb files, they may be misread. This gives the acronym: P for pdb, Q for charge, R for radius.
Jmol Wiki – File formats/Coordinates
Jmol interprets the charge values property partialcharge and the radii property vanderwaalsand can hence use them e. The fileset must have a structure like:. The filter option of the load command can be used, as well as a new option to allow selective “first,last,step” loading of coordinate trajectories. This is preliminary and needs testing. You can see an example. Jmol reads files output from the computational chemistry package Q-Chem. See the Q-Chem specific section.
This format is used e. Any line that starts with will be taken as a comment and it can contain an inline script. Blank lines are ignored. It is somewhat similar to the mol format. Jmol has a limited capability for writing molecular coordinates, including only the currently selected set of atoms. This allows to save the whole model, maybe in a format different from the original one, or to extract a subset of the atoms in the original model.
Due to Java security restraints, only the application and the signed applet can write to files on disk. The unsigned applet can however display the exported data in the console window, from where you can copy it, paste into a text editor and save it to file. The method is to use the write command from script or from the console. Retrieved from ” http: Views Page Discussion View source History.
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