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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You can make changes to your script in the “script” box of Jmol, and rerun the script to view the change, rather than typing it into the Jmol Console. The file extension is not taken into account for identifying the format. Example by Paul Bourke.
File formats/3D Objects
See also show below, as an alternative. Contains atom coordinates and information on biomolecular residues, sequence, chains, hydrogen and disulfide bonds, secondary structure, biologically relevant sites, cofactors. Jmol reads files output from the computational chemistry package Q-Chem. In the dropdown menu, select “Export” and then “Export Image”.
All of the above commands will save the original cooordinates of each atom as they were in the input file. Jmol reads Fxport files.
Supports multi-model data multi-frame, animations. The data can later be loaded using load var a.
This information will be helpful if you decide to create an electronic poster or Proteopedia page to accompany a model.
Example by Paul Bourke, and other example exoort. This format is used e. Insert comments throughout your script. These formats support formal charges and isotopes ; both are read by Jmol.
Remove any “blind alleys” that you took in your model design 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. You can see an example. Contents 1 Exporting or saving molecular model files from Jmol 1. Alternately, ezport can quickly narrow your search by removing the last half of the script, then running the first half.
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. This function in the Jmol Scripting Language allows to place the output of the write command into a variable, rather than saving to a file.
Saving a JPEG of your model design is useful, but it doesn’t save a record ezport the commands you used to obtain the design. Features are nearly identical to those of VRML. Can also contain temperature factor, formal charge, element symbol, alternate locations. You’ll only need the final “color backbone” command that has the actual color of your model.
If you need support for partial charges, see the similar PQR format below.
The fileset must have a structure like:. Retrieved from ” http: This format was originally from the XMol jkol, but has been widely adopted by many other programs.
Saving results from Jmol
Copy and paste this history into a word processor or text editor. Details of HIN format. The 2nd is referenced from the 1st, so you should keep them together for loading into any other software.
Due to Java security restraints, only the application and the signed applet can write to files on disk. After you have completed expott model design, click “history” on the Jmol Console.
Drag and drop your PDB file into Jmol. Jmol can export an image of the model into a pdf document single page, just the image in the center. Note expotr in these OBJ files, atoms are true spheres and not many-faced-polyhedra. Remove the first three lines or so of your script, starting with zap, load file, etc.
Personal tools Log in. Remove any typos that occurred while you were designing your model. Recent versions of Jmol application and signed applet can export models to several formats that specify three-dimensional objects and can be read by specialized software 3D-world or 3D-scenes.