Re: [ccp4bb] Error in assignment of symmetry operators
Dear Gerard, Thank you for the answer, absolutely not a problem! I am very grateful for all the great software from Global Phasing and I know that support is great. Enjoying the STARANISO server for example atm. Best wishes, Radu > Dear Radu, > Nice to know that your problem is sorted and that you are pleased > with the results you are getting from BUSTER. > Clemens had drafted an answer along exactly the same lines and > circulated it around the team for comments, but we were momentarily distracted by something else and the CCP4BB experts beat us to it :-) > I should say that this is not a representative case: we usually > respond quickly and spare no pains to give users the help they need. > With best wishes, > Gerard. > -- > On Tue, Jun 20, 2017 at 05:02:24PM +0100, r...@mrc-lmb.cam.ac.uk wrote: >> Hi Robbie, Pietro, >> Thank you for the quick replies! I tried this before, but must have messed up >> things afterwards somehow... Anyway, tried again and now Buster works beautifully. Indeed the molecule was a couple of unit cells away from the origin, as the error message suggests... My fault. >> Best wishes, >> Radu >> > Hi Radu, >> > This may be caused by the coordinates being too many unit cells away from >> the >> > origin. In COOT you can easily ?symmetry move coordinates here? to a >> place >> closer to the origin. >> > Hope this helps, >> > Robbie >> > Sent from my Windows 10 phone >> > Van: r...@mrc-lmb.cam.ac.uk<mailto:r...@mrc-lmb.cam.ac.uk> >> > Verzonden: dinsdag 20 juni 2017 16:14 >> > Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> >> > Onderwerp: [ccp4bb] Error in assignment of symmetry operators Dear All, >> > Apologies for posting a Buster-related question to this list, the >> buster-discuss one seems less active :-) I am trying to run a refinement job, >> > and hit the following problem: >> > ERROR : [run_buster-0046] unable to create initial SCREEN >> > output with gelly - see >> > refine/01-BUSTER/Cycle-1/gelly_screen.log) >> > Looking in the gelly_screen.log, the problem reported is: >> > Getting symmetry operators from TNT. >> > gelly will classify symmetry using pdb-like convention: >> > SYMOP SYMMETRY >> > NNNMMM OPERATOR >> >1555 X,Y,Z >> >2555 -X,Y,-Z >> >3555 1/2+X,1/2+Y,Z >> >4555 1/2-X,1/2+Y,-Z >> > where NNN -> operator number and MMM -> translation vector >> > *** ERROR in assignment of symmetry operators NNNMMM (M<1 or M>9). *** >> ERROR >> maybe the molecules are far away from the origin. >> > I tried everything I could think of to fix this, no luck so far I'm >> probably making a very silly mistake... But would be very grateful for any advice! >> > Best wishes, >> > Radu >> > PS: space group is C2 >> > -- >> > Radu Aricescu >> > MRC Laboratory of Molecular Biology >> > Francis Crick Avenue >> > Cambridge Biomedical Campus >> > Cambridge CB2 0QH, U.K. >> > tel: +44-(0)1223-267049 >> > fax: +44-(0)1223-268305 >> > www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu
Re: [ccp4bb] Error in assignment of symmetry operators
Dear Radu, Nice to know that your problem is sorted and that you are pleased with the results you are getting from BUSTER. Clemens had drafted an answer along exactly the same lines and circulated it around the team for comments, but we were momentarily distracted by something else and the CCP4BB experts beat us to it :-) I should say that this is not a representative case: we usually respond quickly and spare no pains to give users the help they need. With best wishes, Gerard. -- On Tue, Jun 20, 2017 at 05:02:24PM +0100, r...@mrc-lmb.cam.ac.uk wrote: > Hi Robbie, Pietro, > > Thank you for the quick replies! I tried this before, but must have messed up > things afterwards somehow... Anyway, tried again and now Buster works > beautifully. Indeed the molecule was a couple of unit cells away from the > origin, as the error message suggests... My fault. > > Best wishes, > > Radu > > > > Hi Radu, > > This may be caused by the coordinates being too many unit cells away from > the > > origin. In COOT you can easily ?symmetry move coordinates here? to a place > closer to the origin. > > Hope this helps, > > Robbie > > Sent from my Windows 10 phone > > Van: r...@mrc-lmb.cam.ac.uk<mailto:r...@mrc-lmb.cam.ac.uk> > > Verzonden: dinsdag 20 juni 2017 16:14 > > Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> > > Onderwerp: [ccp4bb] Error in assignment of symmetry operators > > Dear All, > > Apologies for posting a Buster-related question to this list, the > buster-discuss one seems less active :-) I am trying to run a refinement > job, > > and hit the following problem: > > ERROR : [run_buster-0046] unable to create initial SCREEN > > output with gelly - see > > refine/01-BUSTER/Cycle-1/gelly_screen.log) > > Looking in the gelly_screen.log, the problem reported is: > > Getting symmetry operators from TNT. > > gelly will classify symmetry using pdb-like convention: > > SYMOP SYMMETRY > > NNNMMM OPERATOR > >1555 X,Y,Z > >2555 -X,Y,-Z > >3555 1/2+X,1/2+Y,Z > >4555 1/2-X,1/2+Y,-Z > > where NNN -> operator number and MMM -> translation vector > > *** ERROR in assignment of symmetry operators NNNMMM (M<1 or M>9). *** ERROR > maybe the molecules are far away from the origin. > > I tried everything I could think of to fix this, no luck so far I'm > probably making a very silly mistake... But would be very grateful for any > advice! > > Best wishes, > > Radu > > PS: space group is C2 > > -- > > Radu Aricescu > > MRC Laboratory of Molecular Biology > > Francis Crick Avenue > > Cambridge Biomedical Campus > > Cambridge CB2 0QH, U.K. > > tel: +44-(0)1223-267049 > > fax: +44-(0)1223-268305 > > www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu
Re: [ccp4bb] Error in assignment of symmetry operators
Hi Robbie, Pietro, Thank you for the quick replies! I tried this before, but must have messed up things afterwards somehow... Anyway, tried again and now Buster works beautifully. Indeed the molecule was a couple of unit cells away from the origin, as the error message suggests... My fault. Best wishes, Radu > Hi Radu, > This may be caused by the coordinates being too many unit cells away from the > origin. In COOT you can easily symmetry move coordinates here to a place closer to the origin. > Hope this helps, > Robbie > Sent from my Windows 10 phone > Van: r...@mrc-lmb.cam.ac.uk<mailto:r...@mrc-lmb.cam.ac.uk> > Verzonden: dinsdag 20 juni 2017 16:14 > Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> > Onderwerp: [ccp4bb] Error in assignment of symmetry operators > Dear All, > Apologies for posting a Buster-related question to this list, the buster-discuss one seems less active :-) I am trying to run a refinement job, > and hit the following problem: > ERROR : [run_buster-0046] unable to create initial SCREEN > output with gelly - see > refine/01-BUSTER/Cycle-1/gelly_screen.log) > Looking in the gelly_screen.log, the problem reported is: > Getting symmetry operators from TNT. > gelly will classify symmetry using pdb-like convention: > SYMOP SYMMETRY > NNNMMM OPERATOR >1555 X,Y,Z >2555 -X,Y,-Z >3555 1/2+X,1/2+Y,Z >4555 1/2-X,1/2+Y,-Z > where NNN -> operator number and MMM -> translation vector > *** ERROR in assignment of symmetry operators NNNMMM (M<1 or M>9). *** ERROR maybe the molecules are far away from the origin. > I tried everything I could think of to fix this, no luck so far I'm probably making a very silly mistake... But would be very grateful for any advice! > Best wishes, > Radu > PS: space group is C2 > -- > Radu Aricescu > MRC Laboratory of Molecular Biology > Francis Crick Avenue > Cambridge Biomedical Campus > Cambridge CB2 0QH, U.K. > tel: +44-(0)1223-267049 > fax: +44-(0)1223-268305 > www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu
Re: [ccp4bb] Error in assignment of symmetry operators
Hi Radu, This may be caused by the coordinates being too many unit cells away from the origin. In COOT you can easily ‘symmetry move coordinates here’ to a place closer to the origin. Hope this helps, Robbie Sent from my Windows 10 phone Van: r...@mrc-lmb.cam.ac.uk<mailto:r...@mrc-lmb.cam.ac.uk> Verzonden: dinsdag 20 juni 2017 16:14 Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Onderwerp: [ccp4bb] Error in assignment of symmetry operators Dear All, Apologies for posting a Buster-related question to this list, the buster-discuss one seems less active :-) I am trying to run a refinement job, and hit the following problem: ERROR : [run_buster-0046] unable to create initial SCREEN output with gelly - see refine/01-BUSTER/Cycle-1/gelly_screen.log) Looking in the gelly_screen.log, the problem reported is: Getting symmetry operators from TNT. gelly will classify symmetry using pdb-like convention: SYMOP SYMMETRY NNNMMM OPERATOR 1555 X,Y,Z 2555 -X,Y,-Z 3555 1/2+X,1/2+Y,Z 4555 1/2-X,1/2+Y,-Z where NNN -> operator number and MMM -> translation vector *** ERROR in assignment of symmetry operators NNNMMM (M<1 or M>9). *** ERROR maybe the molecules are far away from the origin. I tried everything I could think of to fix this, no luck so far I'm probably making a very silly mistake... But would be very grateful for any advice! Best wishes, Radu PS: space group is C2 -- Radu Aricescu MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. tel: +44-(0)1223-267049 fax: +44-(0)1223-268305 www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu
[ccp4bb] Error in assignment of symmetry operators
Dear All, Apologies for posting a Buster-related question to this list, the buster-discuss one seems less active :-) I am trying to run a refinement job, and hit the following problem: ERROR : [run_buster-0046] unable to create initial SCREEN output with gelly - see refine/01-BUSTER/Cycle-1/gelly_screen.log) Looking in the gelly_screen.log, the problem reported is: Getting symmetry operators from TNT. gelly will classify symmetry using pdb-like convention: SYMOP SYMMETRY NNNMMM OPERATOR 1555 X,Y,Z 2555 -X,Y,-Z 3555 1/2+X,1/2+Y,Z 4555 1/2-X,1/2+Y,-Z where NNN -> operator number and MMM -> translation vector *** ERROR in assignment of symmetry operators NNNMMM (M<1 or M>9). *** ERROR maybe the molecules are far away from the origin. I tried everything I could think of to fix this, no luck so far I'm probably making a very silly mistake... But would be very grateful for any advice! Best wishes, Radu PS: space group is C2 -- Radu Aricescu MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. tel: +44-(0)1223-267049 fax: +44-(0)1223-268305 www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu
