Re: [ccp4bb] JLigand distorts molecules

2012-01-13 Thread Garib N Murshudov
That is interesting. It works for me here and for few other people in other places. Can you exit and restart JLigand, can you send me a figure of what is happening? regards Garib On 13 Jan 2012, at 11:00, Wolfgang Skala wrote: > ccp4 is 6.2.0, > refmac5 is 5.7.0010 (the file you provided; fo

Re: [ccp4bb] JLigand distorts molecules

2012-01-13 Thread Wolfgang Skala
ccp4 is 6.2.0, refmac5 is 5.7.0010 (the file you provided; formerly 5.6.0117), libcheck is 5.2 (formerly 5.1.14), dictionary is 5.28 I also tried each of the four refmac5-libcheck combinations, but without success. yours Wolfgang

Re: [ccp4bb] JLigand distorts molecules

2012-01-13 Thread Garib N Murshudov
That is interesting. Do you use the latest ccp4 and dictionary that comes with it? What are the version of dictionary, libcheck, refmac Just typing refmac5 -i libcheck -i you should get version information. The version of the dictionary is on the top of a file head $CLIBD_MON/list/mon_lib_lis

Re: [ccp4bb] JLigand distorts molecules

2012-01-13 Thread Wolfgang Skala
Dear Garib, thanks for your reply. However, when I use the new versions, 3GP is an apparently random polyhedron which does not resemble 3'-GMP at all. Yours Wolfgang

[ccp4bb] AW: [ccp4bb] JLigand distorts molecules

2012-01-12 Thread Stefan Gerhardt
esendet: 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 on

Re: [ccp4bb] JLigand distorts molecules

2012-01-12 Thread Garib N Murshudov
-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,

Re: [ccp4bb] JLigand distorts molecules

2012-01-12 Thread Boaz Shaanan
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

[ccp4bb] JLigand distorts molecules

2012-01-12 Thread Wolfgang Skala
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