> I am using Jmol version 7, both the application and the applet, and > have a > short wishlist that would make Jmol very useful for X-ray > crystallographers like me: Good ... please send suggestions
> 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! Great! > 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 OK, Patrick or someone is going to have to help me out with this I am already lost :( > 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 - Can you send me a small file that will demonstrate this in the Jmol application? > 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"). Fabian, Egon? > 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 OK, I see that there are atoms outside the cell. Are these the corresponding atoms in the neighboring cells? > Here I display a cell using the chemsymphony applets (I had to build a > PDB file that included "bonds" for the cell edges). Good trick. > I would like to use the Jmol applet to do this. I suspect we can make it work. > 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 I am sure that Egon knows about this. > 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. Hmmm ... that would be interesting. > Finally, if the Jmol applet could also include the ability to measure > distances and angles, that would be very useful. Actually, most of the code is done and is already in the applet ... but there is no good UI for it. Using a RasMol/Chime script you can measure things today. The script command monitor 1 2 will measure the distance between atoms 1 & 2 monitor 1 2 3 will measure the angle between atoms 1, 2, & 3, and monitor 1 2 3 4 will measure the dihedral angle between 1, 2, 3, & 4. > 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! I need suggestions on the UI gestures to do this. Can you tell me what some other packages do? I am thinking of something like this dbl-click to drop an anchor (optionally) click on intermediate atoms dlb-click to end The other problem is where to position the text of the measurement so that it is visible. Do you have any suggestions? Next problem: In your opinion, should the size of the font change with the size of the atoms or not? Finally, we need a way to delete these things. Frankly, I haven't felt like I had good answers to these questions ... and that is why it isn't done. > 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". Hmmm ... this is currently somewhat of a sore spot. I recommend that you familiarize yourself with the RasMol scripting commands that are available in Jmol. To change the size of the hydrogens you need to run the script "select hydrogen; cpk 0.123" That will set the radius of the atoms to 0.123 angstroms. You can run a small script when your applet loads and set the colors and sizes the way you want them. > Thank you and keep up the good work - Jmol is amazing! Glad that you find it useful. We are planning to release a new version of Jmol within the next few weeks. Additionally, we will soon be looking for testers for a major release that has significant changes. Would you be interested in helping out the testing by running the prerelease version? Miguel ------------------------------------------------------- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
