Re: create a disulphide in a protein

11 Feb 2002


      Dear Giulio,
Method 1) should work. It is difficult to know exactly what is 
happening unless you tell us more about the output you get. But a 
common mistake is to use the numbering of the template, instead of the 
numbering of the model, when specifying the RESIDUE_IDS of the residues 
to be patched. In your script, does '298' '303' correspond to the 
numbering of the cysteine residues in the template or the model? It 
should be the numbering in the model.
I hope this helps.
Best,
Roberto
-- 
Roberto Sanchez, Assistant Professor
Structural Biology Program, Department of Physiology & Biophysics and
Institute for Computational Biomedicine, Mount Sinai School of Medicine 
Box 1677, 1425 Madison Avenue, New York, NY 10029
phone +1 (212) 659 8648, fax +1 (212) 849 2456
http://physbio.mssm.edu/~sanchez/


----- Original Message -----
From: Giulio Rastelli giulio@caesar.unimo.it
Date: Monday, February 11, 2002 7:48 am
Subject: create a disulphide in a protein

> Dear Modellers,
> 
> Starting from a Xray structure of a protein where the 2 cysteines 
> are far
> apart, I would like to model the *same* protein with a disulphide.
> I tried manual patching of disulphides in 2 ways, but none seems 
> to work:
> 
> 1) 
> 
> INCLUDE
> SET OUTPUT_CONTROL = 1 1 1 1 1
> SET ALNFILE  = '/lab/giulio/cu/homology/align.pir' 
> SET KNOWNS   = 'alr2'
> SET SEQUENCE = 'dis' 
> SET ATOM_FILES_DIRECTORY = '/lab/giulio/cu/homology'
> SET STARTING_MODEL= 1
> SET ENDING_MODEL  = 12
> SET DEVIATION     = 4.0
> SET RAND_SEED     = -12312
> SET HETATM_IO = on
> CALL ROUTINE = 'model'
> STOP
> SUBROUTINE ROUTINE = 'special_patches'
> PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '298' '303'
> RETURN
> END_SUBROUTINE
> 
> 2)
> 
> READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib'
> READ_PARAMETERS FILE = '$(LIB)/par.lib'
> SET HETATM_IO = on
> READ_MODEL FILE = 'alr2'
> SEQUENCE_TO_ALI ATOM_FILES = 'alr2', ALIGN_CODES= 'alr2'
> SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES 
> 'alr2.ini', ;
>                ALIGN_CODES = ALIGN_CODES 'alr2-ini'
> GENERATE_TOPOLOGY SEQUENCE = 'alr2-ini'
> PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '298' '303'
> TRANSFER_XYZ
> BUILD_MODEL INITIALIZE_XYZ= off
> MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo'
> ENERGY
> 
> Any suggestions? Thank you very much for your help
> (PS I'm using Modeller 6)
> 
> Giulio
> 
> 
>

Roberto Sanchez

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