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 <[email protected]>:
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: [email protected]
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
