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. 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
