-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali@salilab.org; Web http://salilab.org
-----Original Message----- From: Bozidar Yerkovich [mailto:bozidar@salilab.org] Sent: Wednesday, February 26, 2003 4:18 PM To: Andrej Sali Subject: modeller in CCP4 (fwd)
---------- Forwarded message ---------- Date: Fri, 21 Feb 2003 14:32:44 -0300 From: Frederico Moraes Ferreira fredi@if.sc.usp.br To: bozidar@salilab.org Subject: modeller in CCP4
Dear Sir, I have been trying to run Modeller6v2 on the CCP4 interface unsuccessfully. The file $MODINSTALL6v2/script/setmodeller is missing or do not take part of this version anymore. So I am writing to ask you how to overcome this problem for the Modeller6v2 or take a previus Modeller version. Thanks in advance. Frederico Moraes Ferreira
Dear All,
I am a new user to modeller am having a few teething problems. I am trying to align a sequence against an NMR structure of a related protein but am getting an error of
rdpir___648E> Alignment sequence not found in PDB file: 1 ./dva.atm recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
The script file is attached below (and I do have a file ./dva.atm) The sequences in alignment and atm files also match exactly.
>From the manual I was unclear how the options structureX and structureN and so wonder whether there are strict formatting requirements for the pdb entry (some of the pdb is also attached below). I edited the NMR model down to one solution as I couldn't find any info on how modeller deals with NMR models. As a related question if anybody could shed some light on how NMR models are dealt with differently (if at all) compared to say crystallographic models and if multiple NMR models of the same structure can be used as models without inputting each as a separate structure I would be very interested to hear,
Thanks in Advance for your help
Simon Holton,
More ./aln.ali >P1;dva structureX:dva::::::: QEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQNFDDE* >P1;uba sequence:uba::::::: ERYEHQLRQLNDMGFFDFDRNVAAKRRSGGSVQALDSLLNGDV--*
More ./dva.atm
ATOM 1 N GLN A 1 28.264 11.297 6.524 1.00 0.00 ATOM 2 CA GLN A 1 29.549 11.974 6.654 1.00 0.00 ATOM 3 C GLN A 1 30.660 11.272 5.855 1.00 0.00 ATOM 4 O GLN A 1 31.702 11.865 5.591 1.00 0.00 ATOM 5 CB GLN A 1 29.969 12.114 8.135 1.00 0.00 ATOM 6 CG GLN A 1 29.478 13.426 8.785 1.00 0.00 ATOM 7 CD GLN A 1 30.626 14.303 9.317 1.00 0.00 ATOM 8 OE1 GLN A 1 30.822 15.438 8.887 1.00 0.00 ATOM 9 NE2 GLN A 1 31.337 13.724 10.301 1.00 0.00 ATOM 10 H GLN A 1 28.069 11.159 5.506 1.00 0.00 ATOM 11 HA GLN A 1 29.432 12.960 6.205 1.00 0.00 ATOM 12 1HB GLN A 1 29.572 11.270 8.700 1.00 0.00 ATOM 13 2HB GLN A 1 31.051 12.022 8.242 1.00 0.00 ATOM 14 1HG GLN A 1 28.910 14.034 8.087 1.00 0.00 ATOM 15 2HG GLN A 1 28.785 13.199 9.596 1.00 0.00 ATOM 16 1HE2 GLN A 1 31.194 12.757 10.532 1.00 0.00 ATOM 17 2HE2 GLN A 1 32.016 14.236 10.824 1.00 0.00
More ./model_default.top # Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'aln.ali' # alignment filename SET KNOWNS = 'dva' # codes of the templates SET SEQUENCE = 'uba' # code of the target SET ATOM_FILES_DIRECTORY = './' SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 2 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling
**************************************************************
Dr. Simon Holton Laboratory of Molecular Biophysics, Rex Richards Building, Department of Biochemistry, University of Oxford South Parks Road Oxford
Tel: 01865 275379 Fax: 01865 275182
**************************************************************
Hi,
have you tried to rename your structure file, i.e. from dva.atm to dva.pdb?
ralf
======================================= Dr. Ralf Schmid Institute of Cell and Molecular Biology The University of Edinburgh King's Buildings Michael Swann Building 3.14 Edinburgh EH9 3JR
On Mon, 3 Mar 2003, Simon Holton wrote:
> Dear All, > > I am a new user to modeller am having a few teething problems. I am trying > to align a sequence against an NMR structure of a related protein but am > getting an error of > > rdpir___648E> Alignment sequence not found in PDB file: 1 ./dva.atm > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > The script file is attached below (and I do have a file ./dva.atm) The > sequences in alignment and atm files also match exactly. > > >From the manual I was unclear how the options structureX and structureN and > so wonder whether there are strict formatting requirements for the pdb entry > (some of the pdb is also attached below). I edited the NMR model down to > one solution as I couldn't find any info on how modeller deals with NMR > models. As a related question if anybody could shed some light on how NMR > models are dealt with differently (if at all) compared to say > crystallographic models and if multiple NMR models of the same structure can > be used as models without inputting each as a separate structure I would be > very interested to hear, > > > > > Thanks in Advance for your help > > Simon Holton, > > > More ./aln.ali > >P1;dva > structureX:dva::::::: > QEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQNFDDE* > >P1;uba > sequence:uba::::::: > ERYEHQLRQLNDMGFFDFDRNVAAKRRSGGSVQALDSLLNGDV--* > > > > More ./dva.atm > > ATOM 1 N GLN A 1 28.264 11.297 6.524 1.00 0.00 > ATOM 2 CA GLN A 1 29.549 11.974 6.654 1.00 0.00 > ATOM 3 C GLN A 1 30.660 11.272 5.855 1.00 0.00 > ATOM 4 O GLN A 1 31.702 11.865 5.591 1.00 0.00 > ATOM 5 CB GLN A 1 29.969 12.114 8.135 1.00 0.00 > ATOM 6 CG GLN A 1 29.478 13.426 8.785 1.00 0.00 > ATOM 7 CD GLN A 1 30.626 14.303 9.317 1.00 0.00 > ATOM 8 OE1 GLN A 1 30.822 15.438 8.887 1.00 0.00 > ATOM 9 NE2 GLN A 1 31.337 13.724 10.301 1.00 0.00 > ATOM 10 H GLN A 1 28.069 11.159 5.506 1.00 0.00 > ATOM 11 HA GLN A 1 29.432 12.960 6.205 1.00 0.00 > ATOM 12 1HB GLN A 1 29.572 11.270 8.700 1.00 0.00 > ATOM 13 2HB GLN A 1 31.051 12.022 8.242 1.00 0.00 > ATOM 14 1HG GLN A 1 28.910 14.034 8.087 1.00 0.00 > ATOM 15 2HG GLN A 1 28.785 13.199 9.596 1.00 0.00 > ATOM 16 1HE2 GLN A 1 31.194 12.757 10.532 1.00 0.00 > ATOM 17 2HE2 GLN A 1 32.016 14.236 10.824 1.00 0.00 > > More ./model_default.top > # Homology modelling by the MODELLER TOP routine 'model'. > > INCLUDE # Include the predefined TOP routines > > SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file > SET ALNFILE = 'aln.ali' # alignment filename > SET KNOWNS = 'dva' # codes of the templates > SET SEQUENCE = 'uba' # code of the target > SET ATOM_FILES_DIRECTORY = './' > SET STARTING_MODEL= 1 # index of the first model > SET ENDING_MODEL = 2 # index of the last model > # (determines how many models to > calculate) > CALL ROUTINE = 'model' # do homology modelling > > > > > ************************************************************** > > Dr. Simon Holton > Laboratory of Molecular Biophysics, > Rex Richards Building, > Department of Biochemistry, > University of Oxford > South Parks Road > Oxford > > Tel: 01865 275379 > Fax: 01865 275182 > > ************************************************************** > >
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Andrej Sali -
Ralf Schmid -
Simon Holton