Angel, Thanks for the reply, that's very encouraging and I'm happy for you to use this as an example if you think it's interesting.
Using various resources (both on-line and your book) I've put together a very quick "proof of concept" but without any error spheroids, which you'll find at http://www.research.plymouth.ac.uk/pegg/staff/lewis_ca/testing/molecules/3D_plotting.htm. I'm a bit rusty on using Jmol and scripting so what I've done may not be the best way to go about things although I'm pleased it's worked so far. The data are from a spreadsheet, so I've hand edited a small pdb file I created, deleting everything but the atom co-ordinates (again maybe not what I should do). I think the pdb file structure is quite rigid so if I had a lot of data points to do I'd probably create a little formula in the spreadsheet to spit out each data line. I'll need to read up on the structure of the pdb file as I'm not familiar with the parameters you mention, I guess there's something on http://www.pdb.org/... ah a 213 page document at http://www.wwpdb.org/docs.html, so that's going to keep me busy! All in all, I'm having fun and learning something to boot! All the best, Anthony -----Original Message----- From: Angel Herráez [mailto:[email protected]] Sent: 10 June 2009 20:34 To: [email protected] Subject: Re: [Jmol-users] Plotting 3D data with Jmol Anthony, that sounds totally feasible using Jmol You may like to visit http://biomodel.uah.es/Jmol/plots/ Not easy to follow code-wise, but will give you some idea of things that can be done. The issue of the spheroid needs some thought. If the points are few, you may code those using the scripting language. The "errors" can be put into some of the fields e.g. in pdb format, the B-factor (temperature) or the occupancy, and then have Jmol retrieve those into a variable and use them to plot the spheroids using "draw". It's interesting, and I would be willing to help. I am supposed to have a paper written about Jmol for plotting data, but haven't managed to finish it off, so your case mught be another example. How would you produce the files? Will they be the output of some program, or would you code them manually? ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
