[resending this -- attachments were too large] Jmol Developers, -- Eric, Miguel, Jonathan, Egon, Angel, Rolf and others -
I need some feedback here. I think I finally fixed a long-standing bug/feature in Jmol. But I'm open to suggestions if you think I have gone too far in that it WILL change the look of Jmol. (We're talking Jmol 11.10 here, not a fix in 11.8) The problem was noted several years ago, but until today I hadn't figured out how to approach it properly. In a certain sense there is no "right" answer here, but I think this fix will go a long way to making the situation better for more people. The issue has to do with the fact that the Jmol VDW data set was derived from OpenBabel 1.0, which has rather inflated values for H, C, N, and O. These seem to be fine for older PDB files that don't have H atoms, but people notice the difference with small molecules. In addition, over time the Babel data set at their site has been updated, and Jmol is long out of sync with that. I added the OpenBabel 2.1 data set a while back (set defaultVDW BABEL), and today I noticed that there is still another, newer, set associated with OpenBabel 2.2. With the latest code I have checked in you can check this with a new syntax: load caffeine.xyz spacefill JMOL # really old OpenBabel values spacefill BABEL # newest OpenBabel values spacefill BABEL21 # older values; "BABEL" in Jmol 11.8 examples can be found at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm The real problem is that there is no single VDW set that works well with both non-H PDB files and with small molecules or PDB files having H atoms.The JMOL set is nice for non-H PDB files because it accounts for some of the lost H atoms, but it looks quite odd with small molecules, as has been mentioned previously on this list. That's the real problem. My proposed solution is as follows: 1) update the OpenBabel 2.2 set as BABEL 2) move the older OpenBabel 2.1 set as BABEL21, in case someone wants that 3) keep the oldest OpenBabel 1.0 set as JMOL 4) add a "set DEFAULTVDW AUTO" option (which would be the default behavior), which preserves the JMOL default for traditional PDB files having no H atoms but switches to BABEL when hydrogen atoms are present or when the file doesn't have residues. 5) make the default VDW radii model-dependent, so if you open caffeine and 1CRN.PDB and 1CDR.PDB all will look correct. Caffeine and 1CDR will both load using the BABEL set; 1CRN will load using the JMOL set. 6) preserve the current SPACEFILL view as "set defaultVDW JMOL" and the current ball&stick view as "spacefill 20%JMOL" Be assured that all STATE scripts saved to date will restore to their exact previous state -- no change there. However, just reading new files will show a slight difference in size of atoms. I've put up some images so you can see the difference: http://chemapps.stolaf.edu/jmol/docs/img/caffeine-JMOL.png http://chemapps.stolaf.edu/jmol/docs/img/caffeine-BABEL.png http://chemapps.stolaf.edu/jmol/docs/img/caffeine-BABEL21.png Note that the default ball&stick rendering of Jmol was 20%JMOL, so this change of parameters changes the standard ball and stick look as well, not just spacefill 100%. The BABEL set is (appropriately) smaller radii, so I'm suggesting we set the default radius to 23%BABEL. This matches the C radius pretty closely. Compare: spacefill 20%JMOL spacefill 23%BABEL http://chemapps.stolaf.edu/jmol/docs/img/caffeine-JMOL-20percent.png http://chemapps.stolaf.edu/jmol/docs/img/caffeine-AUTO-23percent.png I happen to think the difference is quite subtle, but there is a difference, and I'd like comments about whether you feel it's a big deal or not. Thanks, Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------ This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
