Re: how are these restraints obtained?

[Andras Fiser <>]

Hello,

these are used defined restraints i.e. you get them from any source you
may have: pull out experiments, NMR data,  mutational studies etc or
intelligent guessing.

In this specific case the restraints were obtained by measuring
distances between the substrate and active site residues in various
template structures. These residues and the corresponding distances are
well conserved. Once we had these data we rounded them up a little more
just to give some freedom during modeling and they were defined as upper
limit distances only. More details about it in the original articles:
http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=10339579&form=6&db=m&Dopt=b
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12054650&dopt=Abstract

 details of the command can be found under the 
ADD_RESTRAINT 
command in the manual.


Andras


"michael hanlon (BITS)" wrote:
> 
> Hi folks,
> I am looking at some of the examples provided in the supplementary material, and in particular inclusion of user specified restraints. My question is (i) how are these restraints obtained, (ii) what do the numbers (i.e. RESTRAINT_PARAMETERS)actually refer to. I've looked at the manual but am not much the wiser.  Here's the script:
> --------------------------------------------------------------------------------
> INCLUDE
> SET OUTPUT_CONTROL =  1 1 1 1 1
> SET ATOM_FILES_DIRECTORY = '/usr/users/hanlon/Modeller/modeller6v1/atom_files'
> SET ALNFILE = 'TvLDH-4mdh-1emd_ed.ali'
> SET KNOWNS = '4mdhA' '1emd_ed'
> SET SEQUENCE = 'TvLDH'
> SET STARTING_MODEL = 1
> SET ENDING_MODEL = 5
> SET HETATM_IO = on
> CALL ROUTINE = 'model'
> 
> SUBROUTINE ROUTINE = 'special_restraints'
> #ADD_RESTRAINT ATOM_IDS =  'NH1:161' 'O1A:335',; #            RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1 #ADD_RESTRAINT ATOM_IDS =  'NH2:161' 'O1B:335',; #            RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1 #ADD_RESTRAINT ATOM_IDS =  'NE2:186' 'O2:335',; #            RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1
> ADD_RESTRAINT ATOM_IDS =  'NH1:161' 'O1A:334',;
>             RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1
> ADD_RESTRAINT ATOM_IDS =  'NH2:161' 'O1B:334',;
>             RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1
> ADD_RESTRAINT ATOM_IDS =  'NE2:186' 'O2:334',;
>             RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1
> 
> RETURN
> END_SUBROUTINE
> --------------------------------------------------------------------------------]
> Any help much appreciated,
> 
> Mike

-- 
    ,
Andras Fiser, PhD            # phone: (212) 327 7216
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras