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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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.
Here is a list of format values. Jmol reads Cube files, original from Gaussian software Gaussian website. Example by Paul Bourke, and other rxport files. Jmol reads files output from the computational chemistry package Q-Chem. Expoort follows is a expport of specifications and comments on several formats, but is not a complete listing of all formats supported. Jmol can export an image of the model into a pdf document single page, just the image in the center.
This is preliminary and needs testing. It is not a good idea to save over your earlier designs! P for pdb, Q for charge, R for radius.
Blank lines are ignored. An extension of this format supports isotopesand they are read by Jmol. Details of HIN format.
There is also the choice only in MOL format of saving the transformed coordinates as they are in the current state of the model:. Description by Paul Bourke.
Saving results from Jmol
Be sure to include the following information in your Word document expot saving: Example files supported by Jmol. Jmol can get files directly from the Protein Data Bank website.
After annotating your script, you should always run the script to make sure there aren’t any errors. Wikipedia info on Maya. Retrieved from ” expor Feel free to add a subsection with a description of a format you know well. Alchemy example and Alchemy description by Paul Bourke. This gives the acronym: Jmol can get files directly from the ligand collection at the Protein Data Bank website.
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. Contains atom coordinates and information on biomolecular residues, sequence, chains, hydrogen and disulfide bonds, secondary structure, biologically relevant sites, cofactors. In the dropdown menu, select “Export” and then “Export Image”. Contains only atom coordinates no bonds and, optionally, charges and vectors e.
Remove any “blind alleys” that you took in your model design Also, force vectors are read and included as vibrations activated by default on file load. Contains atom coordinates and bonds. There are example files of Gaussian input, output and log. The syntax see reference documentation is like this:.
A simple Alchemy reader is implemented starting Jmol Jmkl line that starts with will be taken as a comment and it can contain an jmpl script.
Can also contain temperature factor, formal charge, element symbol, alternate locations. Views Page Discussion View source History. See also show below, as an alternative. Jmol interprets the charge values property partialcharge and the radii property vanderwaalsand can hence use them e.
In this jmpl, Jmol is in fact exporting file formats that it cannot export natively, by using the format conversion server at NCI. If the materials file is missing your model will be monochrome.
Here is a sample script before and after annotating. Jmol reads mmCIF files. The most interesting feature of this format is that it can be embedded in pdf filesproviding a 3D experience inside this well established standard for publication.