Dear colleagues, has anyone of you experienced problems regarding regularization in JLigand? When I start the first tutorial and load 3'-GMP (3GP), the double bond to the O6 atom is about twice as long as the remainder of the molecule; the rings are also highly distorted. Similarly, if I modify a ligand, regularization yields a structure that is definitely out of shape.
I'm using JLigand 1.0.25 on Ubuntu 11.10 and tried both the current version of OpenJDK and Sun Java JRE 6u30; even compiling the JLigand source on my platform with Sun Java SE 6u30 did not help. Kind regards, Wolfgang Skala -- Structural Biology Group / Department of Molecular Biology University of Salzburg Billrothstraße 11 5020 Salzburg Austria Phone: +43 662 8044 7278 http://www.uni-salzburg.at/xray
