Rolf Huehne wrote: > Hi all, > >I noticed an unexpected way of Jmol to render aromatic bonds. > >I would expect that all bonds in an aromatic ring would be drawn >identically. This would mean all dotted lines at the inner side and all >solid lines at the outer side. > >But Jmol places the dotted lines sometimes at the outer and sometimes at >the inner side. In rare cases all dotted lines are at the inner side but >most of the time several ones are at the outer side. > > > I'll look into this. But it is a VERY difficult problem, actually.
>You can see an example image here: > http://www.fli-leibniz.de/ImgLibPDB/tmp/061.png > >The image was generated using the following CIF file: > http://www.fli-leibniz.de/ImgLibPDB/tmp/061.cif > >And since Jmol ignores the bond order information in CIF files the >following script has explicitly set the bond order using connect commands: > http://www.fli-leibniz.de/ImgLibPDB/tmp/061.jmz > >After I have read Bob's recent explanation on bond orders in Jmol > > >>OK, here is a total generalization of partial bonds. With this (11.3.28) >>you can draw any type of partial whatever up to 5 bonds. Works in >>bondOrder and connect, both: >> >> bondorder partial N.M >> connect (atomexpr1) (atomexpr2) partial N.M >> >>where N is the number of bonds you want (1-5) >>and M is a "bitmask" indicating which of those lines you want dotted. >> >>You have to work in binary for this: >> >>M binary meaning >>0 00000 no lines dotted >>1 00001 first line dotted >>2 00010 second line dotted >>3 00011 first and second line dotted >>4 00100 third line dotted >>.... >>31 11111 all (five) lines dotted >> >> >> >I tried to change the order of the atoms in the connect commands in >order to change which line is considered the first one. But there was no >difference. > >Q: Do others also consider this as a bug? > >Q: Is there any way to influence which line is considered the first one? > >---- Test System ---------------- > Jmol: 11.3.25, application > Java: 1.5.0_12 > OS : Linux, OpenSuSE 10.2 >--------------------------------- > >Regards, >Rolf > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. >Still grepping through log files to find problems? Stop. >Now Search log events and configuration files using AJAX and a browser. >Download your FREE copy of Splunk now >> http://get.splunk.com/ >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
