Dear Giulio,
The log file contains the following error message:
rdpir___270E> Error reading/processing file:
/lab/giulio/cu/homology/align.pir
which means Modeller had trouble reading your alignment file. The
alignment file looks like this:
>P1;alr2
structure:alr2:1 : :316 : : ::-1.00:-1.00
ASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIV
SKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDE
GLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDP
SLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCAL
LSCTSHKDYPFHEEF/.
>P1;dis
sequence:dis:1 : :316 : : ::-1.00:-1.00
ASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIV
SKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDE
GLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDP
SLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCAL
LSCTSHKDYPFHEEF/.
The end of sequence in Modeller should be marked by '*', not '.'. That's
why Modeller can't read the alignment file and doesn't produce any
output.
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/
Giulio Rastelli wrote:
>
> Dear Roberto,
> thanks for your reply. In my case, residue numbers of template and model
> are the same, as I am just modeling the *same* protein with the only
> difference that the template does not have a disulphide, while a disulphide
> is requested in the model. I attach the .top and .log files.
> Thank you very much again
>
> Giulio
>
> At 08.49 11/02/02 -0500, you wrote:
> >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 <>
> >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
> >>
> >>
> >>
> >
> >
>
> ------------------------------------------------------------------------
> Name: align.pir
> align.pir Type: Plain Text (text/plain)
> Encoding: 7BIT
>
> Name: model.top
> model.top Type: Plain Text (text/plain)
> Encoding: 7BIT
>
> Name: model.log
> model.log Type: Plain Text (text/plain)
> Encoding: 7BIT
>
> ------------------------------------------------------------------------
>
> Giulio Rastelli
> Dipartimento di Scienze Farmaceutiche
> Università di Modena e Reggio Emilia
> Via Campi 183, 41100 Modena, ITALY
> tel 0039-059-2055145 fax 0039-059-2055131