not on my machine (Suse11.3) Jligand (1.0.25) -> Load Ligand -> type "3GP" -> the ligand looks totally normal, incl the C6,O6 double bond.
Cheers Stefan -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Boaz Shaanan Gesendet: Donnerstag, 12. Januar 2012 13:44 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] JLigand distorts molecules Hi, You are right. I happen to have 1.0.7 lying around and there 3GP is fine. A bug must have been introduced somewhere on the way between versions. I wonder whether it's only 3GP. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Wolfgang Skala [wolfgang.sk...@sbg.ac.at] Sent: Thursday, January 12, 2012 1:52 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] JLigand distorts molecules 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
