As far as I can tell, the Jmol applet is the only applet in the known world that will display a unit cell on a webpage (by using a shelxl.res file as input). And it is beautiful!
But, for showing unit cells of molecular compounds (rather than just ionic compounds), it is necessary that you be able to draw all the molecules that extend into neighboring cells and, apparently, this can't be done in the applet (though it can be done using the Jmol application by choosing "original atoms only" under "Crystal Properties" on the "Extras" menu - tho in the application, it would be nice if all the bonds outside the cell would also be drawn automatically instead of by adjusting the "Bond Box"). To see an example of what I'm trying to do, go to the following page on my website:
macxray.chem.upenn.edu/sneddon.html
Here I display a cell using the chemsymphony applets (I had to build a PDB file that included "bonds" for the cell edges). I would like to use the Jmol applet to do this.
My wish for Jmol would also include another type input file - the CIF. This is a "Crystallographic Information File" which is the most popular way of archiving X-ray crystallographic structures - most chemical journals require submission of the CIF with any publication that includes an X-ray structure. With the CIF as input, Jmol would have available to it the estimated errors in the atom coordinates, so when the Jmol application is used to measure a bond distance or angle, it could display the estimated error (which is very important in crystallographic publications) as a number like "1.542(3) A", where the "(3)" indicates the estimated error is .003 A.
Finally, if the Jmol applet could also include the ability to measure distances and angles, that would be very useful. I include the PDB file and the CIF on my website for all users' structures. So if the Jmol applet had these facilities, a user could explore all the important geometrical features of his structures - bond distances, bond angles, hydrogen bonding, crystal packing diagrams, etc. And he could do this using just his web browser without acquiring any other software! AND there is very little software available for individual X-ray structure users to do these sorts of calculations even on there local machine without the use of the web!!
I have noticed one "bug" in the Jmol application - I'm not able to change any of the "atom properties" available on the "Edit" menu. One of the things I would like to do is draw the hydrogen atoms smaller than they are done now. This could be done by adjusting the van der Waals radius in "atom properties".
Thank you and keep up the good work - Jmol is amazing!
Pat Carroll
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