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:[log in to unmask]] Im Auftrag von Boaz Shaanan
Gesendet: Donnerstag, 12. Januar 2012 13:44
An: [log in to unmask]
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: [log in to unmask]
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Wolfgang Skala [[log in to unmask]]
Sent: Thursday, January 12, 2012 1:52 PM
To: [log in to unmask]
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
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