Re: [modeller_usage] Problems with cis proline

[Modeller Caretaker <modeller-care@ucsf.edu>]

Eva María Priego wrote:
> I need to build models of a protien with a disulphide bond beetween 
> monomers, four cis Proline and an aditional helix. I am using Modller 
> 7v7.
...
> The problem is the models obtained don't fit this script, I mean, none 
> of them have the alpha helix and none have the four correct cis proline( 
> or have  more residues in cis) but they have the disulphide bond.What am 
> I doing wrong?.

You should put all of your commands to create special restraints within 
one 'special_restraints' routine. If you define the routine multiple 
times, only the last definition will take effect. You should probably 
use something like the following instead:

SUBROUTINE ROUTINE = 'special_restraints'
SET ADD_RESTRAINTS = 'on'
MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '127:' '149:'
MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '284:' '306:'
CALL ROUTINE = 'cispeptide', ;
               ATOM_IDS1 = 'O:101' 'C:101' 'N:102' 'CA:102', ;
               ATOM_IDS2 = 'CA:101' 'C:101' 'N:102' 'CA:102'
CALL ROUTINE = 'cispeptide', ;
               ATOM_IDS1 =  'O:103' 'C:103' 'N:104' 'CA:104', ;
               ATOM_IDS2 = 'CA:103' 'C:103' 'N:104' 'CA:104'
(etc.)
RETURN
END_SUBROUTINE

	Ben Webb, Modeller Caretaker
--
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage