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
