Yes, it can be done. I may be able to do it soon. I have to find a better delimiter, + may not be good becuase it may be part of atom names. Another way would be: if you have more than 10-15 atoms then you can divide planes into several overlapping planes And yet another way (perhaps better way for large planes): describe planes with all possible local torsion angles with 0 or 180 degree target.
regards Garib On 29 Nov 2012, at 10:36, andrea.p...@unina.it wrote: > Thank you very much to all of you for your replies. > The external restraints mechanism works perfectly as far as you do not exceed > 468 characters in a string. If one wants to restraint more than let's say 15 > atoms it is not feasible! > > Is it possible to list the atoms in a more compact way? I have in mind > something like: > first atom CA chain A residue 25 next atom CB+C+O+X1+X2 chain B residue 50 > or something similar. > > Thank you again for your help. > > Andrea > > > > Quoting Garib N Murshudov <ga...@mrc-lmb.cam.ac.uk>: > >> Dear Andrea >> >> There are two ways as they were mentioned by Tim and Ian: >> 1) Using external restraints mechanism. You define something like (it is an >> example): >> >> external plane first atom CA chain A residue 25 next atom CB chain B residue >> 50 next atom OG chain B residue 100 next atom CC chain C residue 2 sigma 0.02 >> >> You need to add one line per plane. It is better to define these restraints >> in a file and then read in external keywords part of the refmac5 interface >> of ccp4i >> >> 2) Define link and use planes there. Links are defined for pairs of >> residues. The best way of defining links is using JLigand that can be >> downloaded from (it should be available from ccp4 6.3 also): >> >> http://www.ysbl.york.ac.uk/mxstat/JLigand/index.html >> >> there are very good tutorials written by Andrey Lebedev for new ligands as >> well as how to define links and use them in refmac >> >> regards >> Garib >> >> >> On 28 Nov 2012, at 07:03, Andrea Pica wrote: >> >>> Hi everybody! >>> >>> Is there a simple way in REFMAC to restraints a group of atoms belonging to >>> different residues to lay on a plane? Of course I would like to set the >>> sigma! >>> >>> Do I have to add any line in the PDB header? Is it that simple? >>> >>> Thank you very much! >>> >>> Andrea >>> >>> >>> Andrea Pica, Ph.D. student >>> University of Naples "Federico II" >>> Department of Chemical Sciences - Room 1N-04 >>> Complesso Universitario Monte S. Angelo >>> Via Cintia >>> I-80126 Naples - Italy >>> Phone 39-081 674269 >>> Fax 39-081 674090 >> >> Dr Garib N Murshudov >> Group Leader, 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 >> >> >> >> >> > > > > Andrea Pica, Ph.D. student > University of Naples "Federico II" > Department of Chemical Sciences - Room 1N-04 > Complesso Universitario Monte S. Angelo > Via Cintia > I-80126 Naples - Italy > Phone 39-081 674269 > Fax 39-081 674090 > Dr Garib N Murshudov Group Leader, 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
