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 <[log in to unmask]>:
> 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: [log in to unmask]
> 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
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