On Thursday 25 September 2003 17:34, Miguel wrote: > > 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 :(
Yes, I've discussed this in the past with the author of the crystal rendering (Fabian)... this is indeed much needed for molecular crystals, but I have not been able to explain Fabian what I would like to see (never tried with a screenshot...), not have I been able to understand his code in such detail to be able to add that feature... > > 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? e.g. estron.cml in jmol/samples... compare default display with "original atoms only"... > > 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? See above... Ultimately, one would like Jmol to display connected moelcules, but located such the the centre of mass of the molecule is within the crystal 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 > > 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. Please send me an example CIF file, then I'll write a reader for it... > > 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. This is the temperature factor right? Some weeks ago we discussed ortep atoms, but temperature factors we could also display using a coloring scheme... > > 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. Could not find it... what the URL? Egon -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 ------------------------------------------------------- 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
