I just checked in code to change the behavior of ssbonds (and hbonds)
* When you say 'set ssbonds backbone' then the bonds are *no longer* drawn between the two sulphur atoms
* With either 'ssbonds' or 'hbonds', when they are moved to the backbone (set ssbonds/hbonds backbone), if the bond does not have an explicit color assigned, then it will inherit the colors of the original atoms, not the colors of the alpha-carbon atom on the backbone.
I think this will give the desirable default behavior.
Yes, it works great for ssbonds, and hbonds move to desired positions, too. (but color hbonds type is not implemented)
there is still a problem on 500MB RAM Linux2.4.21 Mozilla1.7b java 1.3.2_04 with lots of applet buttons, e.g.
http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1olp
mozilla dumped with the error:
Allocating more space for read msg 338
INTERNAL ERROR on Browser End: Could not register plugininstance
System error?:: Success
on 250MB XP mozilla hang if two such big instances were loaded e.g. 1sos and 1olp Regards, Jan
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