In the current version there is a bug and we have fixed it (as far as i know). It is not JLigand bug, it is libcheck bug. If you take the version (5.7 version) then it may work better.
http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/ You need refmac5.7_linux.tar.gz or refmac5.7_macintelt.tar.gz After gunzipping you need to copy refmacgfortran and libcheckgfortran to $CBIN. It would be better if you keep older version so that you can change back if something happens cp $CBIN/refmac5 $CBIN/refmac5.6 cp refmacgfortran $CBIN/refmac5 cp $CBIN/libcheck $CBIN/libcheck5.6 cp libcheckgfortran $CBIN/libcheck If it also does not work please let me know Cheers Garib On 12 Jan 2012, at 12:43, Boaz Shaanan wrote: > 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 Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
