------ Forwarded Message From: Mario Garcia sbioi000@cib.csic.es Date: Fri, 21 Mar 2003 16:53:17 +0100 (CET) To: modeller-care@salilab.org Subject: Modeller6v2 trouble
Dear Dr. Bozidar, I have some error after a modeling jot execution (mod script.top) in Modeller6v2 under an IRIX 6.2 box. Bellow, I include the corresponding .top and .ali input files and the resulting .log file. Could you give some hints to help me? Thank you very much in advance for your help. Regards, Mario Garcia.
------------------------------------------------------------------------- Mario Garcia de Lacoba, PhD. Phone : +341 915611800 (ext.4334) Fax : +341 915627518 Centro de Investigaciones Biologicas E-mail : mario@cib.csic.es C.S.I.C. c/ Velazquez, 144 28006-Madrid. SPAIN. -------------------------------------------------------------------------
======================MOB3.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 = 'MOB4.ali' # alignment filename SET KNOWNS = '1cii' # codes of the templates SET SEQUENCE = '1mob' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CHECK_ALIGNMENT CALL ROUTINE = 'model' # do homology modelling
================MOB4.ali================================ C; mob_1cii.phy align >P1;1cii structureX:1cii EIMAVDIYVNPPRVDVFHGTPPAWSSFGNKTIWGGNEWVDDSPTRSDIEK RDKEITAYKNTLSAQQKENENKRTEAGKRLSAAIAAREKDENTLKTLRAG NADAADITRQEFRLLQAELREYGFRTEIAGYDALRLHTESRMLFADADSL RISPREARSLIEQAEKRQKDAQNADKKAADMLAEYERRKGILDTRLSELE KNGGAALAVLDAQQARLLGQQTRNDRAISEARNKLSSVTESLNTARNALT RAEQQLTQQKNTPDGKTIVSPEKFPGRSSTNDSIVVSGDPRFAGTIKITT SAVIDNRANLNYLLSHSGLDYKRNILNDRNPVVTEDVEGDKKIYNAEVAE WDKLRQRLLDARNKITSAESAVNSARNNLSARTNEQKHANDALNALLKEK ENIRNQLSGINQKIAEEKRKQDELKATKDAINFTTEFLKSVSEKYGAKAE QLAREMAGQAKGKKIRNVE-EALKTYEKYRADINKKINAKDRAAIAAALE SVKLSDISSNLNRFSRGLGYAGKFTSLADWITEFGKAVRTENWRPLFVKT ETIIAGNAATALVALVFSILTGSALGIIGYGLLMAVTGALIDESLVEKAN KFW* >P1;1mob sequence:1mob ------MSYMVARMQKMKAGNLGGAFKHNERVFETHSNKDINPSRSHLN- --YELTDRDRSVSYEKQIKDYVNENKVSNRAIRKDAVLCDEWIITSDKD- -----------FFEKLDEEQTRTFFETAKNYFAENYG-ESNIAYASVHLD ESTPHMHMGVVPFENGKLSSKAMFDREELKHIQEDLPR--YMSDHGFELE -------------------------------RGKLNSEAKHKTVAEFKRA MADMELKEELLEKYHAPLFVDERTG--ELNNDTEAFWHEKEFADMFEVQS PIRETTNQEKMDWLRKQYQEELKKLESSKKP-LEDDLSHLEELLDKKTKE YIKIDSEASERASELSKAEGYINTLEN--HSKSLEAKIECLESDNLQLEK Q----KATKLEAKALNES----ELRELKPKKNFLGKEHYELSPEQ---FE GLKAEVYRSRTLLHHKDIELEQAKRQVSLRASKNYFTASLERAKEKAKGE SIDR--LKSEIKRLKN------------E----N-SILRQQNDK-MLGKL RELMPDKAFKNLLSELKAIKP-----------IVNIIKKAIEKSLF---- ---*
=====================MOB4.log================================= MODELLER 6v2, 17 Feb 2002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2002 Andrej Sali All Rights Reserved
Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, IRIX64 akilonia 6.5 IP30 Date and time of compilation : 07/05/2002 17:12:26 Job starting time (YY/MM/DD HH:MM:SS): 2003/03/21 23:47:53.033
TOP_________> 105 705 SET ALNFILE = 'MOB4.ali'
TOP_________> 106 706 SET KNOWNS = '1cii'
TOP_________> 107 707 SET SEQUENCE = '1mob'
TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files'
TOP_________> 109 709 SET STARTING_MODEL = 1
TOP_________> 110 710 SET ENDING_MODEL = 1
TOP_________> 111 711 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND check_a_335E> No alignment. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099 Starting time : 2003/03/21 23:47:53.033 Closing time : 2003/03/21 23:48:02.202 Total CPU time [seconds] : 0.00
------ End of Forwarded Message
Maybe it is the missing s in
etenv EXECUTABLE_TYPE6v0 iris4d
?
Best, Andrej
-- 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: owner-modeller_usage@salilab.org > [mailto:owner-modeller_usage@salilab.org] On Behalf Of Modeller Care > Sent: Friday, March 21, 2003 7:57 AM > To: modeller_usage@salilab.org > Subject: FW: Modeller6v2 trouble > > > > ------ Forwarded Message > From: Mario Garcia sbioi000@cib.csic.es > Date: Fri, 21 Mar 2003 16:53:17 +0100 (CET) > To: modeller-care@salilab.org > Subject: Modeller6v2 trouble > > > Dear Dr. Bozidar, > I have some error after a modeling jot execution (mod > script.top) in Modeller6v2 under an IRIX 6.2 box. Bellow, I > include the corresponding .top and .ali input files and the > resulting .log file. Could you give some hints to help me? > Thank you very much in advance for your help. Regards, > Mario Garcia. > > -------------------------------------------------------------- > ----------- > Mario Garcia de Lacoba, PhD. Phone : +341 > 915611800 (ext.4334) > Fax : +341 915627518 > Centro de Investigaciones Biologicas E-mail : mario@cib.csic.es > C.S.I.C. > c/ Velazquez, 144 > 28006-Madrid. SPAIN. > -------------------------------------------------------------- > ----------- > > > ======================MOB3.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 = 'MOB4.ali' # alignment filename > SET KNOWNS = '1cii' # codes of the templates > SET SEQUENCE = '1mob' # code of the target > SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories > for input atom files > SET STARTING_MODEL= 1 # index of the first model > SET ENDING_MODEL = 1 # index of the last model > # (determines how many models to > calculate) > CHECK_ALIGNMENT > CALL ROUTINE = 'model' # do homology modelling > > > > ================MOB4.ali================================ > C; mob_1cii.phy align > >P1;1cii > structureX:1cii EIMAVDIYVNPPRVDVFHGTPPAWSSFGNKTIWGGNEWVDDSPTRSDIEK > RDKEITAYKNTLSAQQKENENKRTEAGKRLSAAIAAREKDENTLKTLRAG > NADAADITRQEFRLLQAELREYGFRTEIAGYDALRLHTESRMLFADADSL > RISPREARSLIEQAEKRQKDAQNADKKAADMLAEYERRKGILDTRLSELE > KNGGAALAVLDAQQARLLGQQTRNDRAISEARNKLSSVTESLNTARNALT > RAEQQLTQQKNTPDGKTIVSPEKFPGRSSTNDSIVVSGDPRFAGTIKITT > SAVIDNRANLNYLLSHSGLDYKRNILNDRNPVVTEDVEGDKKIYNAEVAE > WDKLRQRLLDARNKITSAESAVNSARNNLSARTNEQKHANDALNALLKEK > ENIRNQLSGINQKIAEEKRKQDELKATKDAINFTTEFLKSVSEKYGAKAE > QLAREMAGQAKGKKIRNVE-EALKTYEKYRADINKKINAKDRAAIAAALE > SVKLSDISSNLNRFSRGLGYAGKFTSLADWITEFGKAVRTENWRPLFVKT > ETIIAGNAATALVALVFSILTGSALGIIGYGLLMAVTGALIDESLVEKAN > KFW* > >P1;1mob > sequence:1mob > ------MSYMVARMQKMKAGNLGGAFKHNERVFETHSNKDINPSRSHLN- > --YELTDRDRSVSYEKQIKDYVNENKVSNRAIRKDAVLCDEWIITSDKD- > -----------FFEKLDEEQTRTFFETAKNYFAENYG-ESNIAYASVHLD > ESTPHMHMGVVPFENGKLSSKAMFDREELKHIQEDLPR--YMSDHGFELE > -------------------------------RGKLNSEAKHKTVAEFKRA > MADMELKEELLEKYHAPLFVDERTG--ELNNDTEAFWHEKEFADMFEVQS > PIRETTNQEKMDWLRKQYQEELKKLESSKKP-LEDDLSHLEELLDKKTKE > YIKIDSEASERASELSKAEGYINTLEN--HSKSLEAKIECLESDNLQLEK > Q----KATKLEAKALNES----ELRELKPKKNFLGKEHYELSPEQ---FE > GLKAEVYRSRTLLHHKDIELEQAKRQVSLRASKNYFTASLERAKEKAKGE > SIDR--LKSEIKRLKN------------E----N-SILRQQNDK-MLGKL > RELMPDKAFKNLLSELKAIKP-----------IVNIIKKAIEKSLF---- > ---* > > =====================MOB4.log================================= > MODELLER 6v2, 17 Feb 2002 > > PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS > > > Copyright(c) 1989-2002 Andrej Sali > All Rights Reserved > > Written by A. Sali > with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, > B. Jerkovic, A. Badretdinov, F. Melo, > J.P. Overington & E. Feyfant > Rockefeller University, New York, USA > Harvard University, Cambridge, USA > Imperial Cancer Research Fund, London, UK > Birkbeck College, University of London, London, UK > > > Kind, OS, HostName, Kernel, Processor: 4, IRIX64 akilonia 6.5 IP30 > Date and time of compilation : 07/05/2002 17:12:26 > Job starting time (YY/MM/DD HH:MM:SS): 2003/03/21 23:47:53.033 > > TOP_________> 105 705 SET ALNFILE = 'MOB4.ali' > > TOP_________> 106 706 SET KNOWNS = '1cii' > > TOP_________> 107 707 SET SEQUENCE = '1mob' > > TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files' > > TOP_________> 109 709 SET STARTING_MODEL = 1 > > TOP_________> 110 710 SET ENDING_MODEL = 1 > > TOP_________> 111 711 CHECK_ALIGNMENT > > check_a_343_> >> BEGINNING OF COMMAND > check_a_335E> No alignment. > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Dynamically allocated memory at finish [B,kB,MB]: > 2200483 > 2148.909 2.099 > Starting time : 2003/03/21 > 23:47:53.033 > Closing time : 2003/03/21 > 23:48:02.202 > Total CPU time [seconds] : 0.00 > > > ------ End of Forwarded Message >
Hi, All
I am wondering if it is possible to model a dimer structure from a dimer template. I can not find anything in the manual. I tried to model each of them first and then put them together. However, I am not sure it is good or not for the packing in the contact region. Thanks for your help.
Difei
Sure, you can model a multimer on a multimer template, this is normally to be preferred over putting individually modelled monomers together. Simply align the whole multimer with appropriate chain breaks in the alignment. best, m.
----- Original Message ----- From: "Difei Wang" dwang@nd.edu To: "Andrej Sali" sali@salilab.org Cc: "'Modeller Care'" modeller-care@salilab.org; modeller_usage@salilab.org Sent: Thursday, June 12, 2003 10:34 AM Subject: dimer model
> Hi, All > > I am wondering if it is possible to model a dimer structure from a dimer > template. > I can not find anything in the manual. I tried to model each of them first and > then > put them together. However, I am not sure it is good or not for the packing in > the > contact region. Thanks for your help. > > Difei > Margot Ernst modelling at www.univie.ac.at/brainresearch margot.ernst@univie.ac.at
Hi,
If you have a dimer as template and want to model a dimer with the same organisation, you just need to include a "/" character as chain breaker in the alignment file (between your 2 monomers).
I join an exemple of alignment for a dimer.
On Thu, 12 Jun 2003, Difei Wang wrote:
> Hi, All > > I am wondering if it is possible to model a dimer structure from a dimer > template. > I can not find anything in the manual. I tried to model each of them first and > then > put them together. However, I am not sure it is good or not for the packing in > the > contact region. Thanks for your help. > > Difei > >
>P1;to_model sequence:to_model:1:A:218:B:::: --RLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAP IYTNVTYPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQDSRLPSEFDL SAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQISDFHVATRFNDDFSRAVLEAA / --RLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAP IYTNVTYPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQDSRLPSEFDL SAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQISDFHVATRFNDDFSRAVLEAA*
>P1;template structureX:template:1:A:224:B: : : : VTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGY DAPIYTNVTYPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQDSRLPSE FDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQISDFHVATRFNDDFSRAVLEACV / VTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGY DAPIYTNVTYPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQDSRLPSE FDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQISDFHVATRFNDDFSRAVLEACV*
... and maybe also you have to specify the numeration of the residues in the alignment file
>P1;1cii structureX:1cii like >P1;1cii structureX:1cii:start::end:::::
and check if you have chain in the pdb...
Hope it helps
(and also the war will end soon)
Luca
-------------------------------------------------------- Luca Settimo, Ph.D. Student
Molecular Structures and Biocomputing Department of Biochemistry and Pharmacy Åbo Akademi University Tykistökatu 6A 20520 Turku Finland phone: +358-2-215-4600 fax: +358-2-2153280 mailto:lsettimo@abo.fi Webpage URL http://www.abo.fi/~lsettimo --------------------------------------------------------
Modeller Care wrote:
> ------ Forwarded Message > From: Mario Garcia sbioi000@cib.csic.es > Date: Fri, 21 Mar 2003 16:53:17 +0100 (CET) > To: modeller-care@salilab.org > Subject: Modeller6v2 trouble > > Dear Dr. Bozidar, > I have some error after a modeling jot execution (mod script.top) in > Modeller6v2 under an IRIX 6.2 box. Bellow, I include the corresponding > .top and .ali input files and the resulting .log file. Could you give some > hints to help me? Thank you very much in advance for your help. > Regards, > Mario Garcia. > > ------------------------------------------------------------------------- > Mario Garcia de Lacoba, PhD. Phone : +341 915611800 (ext.4334) > Fax : +341 915627518 > Centro de Investigaciones Biologicas E-mail : mario@cib.csic.es > C.S.I.C. > c/ Velazquez, 144 > 28006-Madrid. SPAIN. > ------------------------------------------------------------------------- > > ======================MOB3.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 = 'MOB4.ali' # alignment filename > SET KNOWNS = '1cii' # codes of the templates > SET SEQUENCE = '1mob' # code of the target > SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom > files > SET STARTING_MODEL= 1 # index of the first model > SET ENDING_MODEL = 1 # index of the last model > # (determines how many models to > calculate) > CHECK_ALIGNMENT > CALL ROUTINE = 'model' # do homology modelling > > ================MOB4.ali================================ > C; mob_1cii.phy align > >P1;1cii > structureX:1cii > EIMAVDIYVNPPRVDVFHGTPPAWSSFGNKTIWGGNEWVDDSPTRSDIEK > RDKEITAYKNTLSAQQKENENKRTEAGKRLSAAIAAREKDENTLKTLRAG > NADAADITRQEFRLLQAELREYGFRTEIAGYDALRLHTESRMLFADADSL > RISPREARSLIEQAEKRQKDAQNADKKAADMLAEYERRKGILDTRLSELE > KNGGAALAVLDAQQARLLGQQTRNDRAISEARNKLSSVTESLNTARNALT > RAEQQLTQQKNTPDGKTIVSPEKFPGRSSTNDSIVVSGDPRFAGTIKITT > SAVIDNRANLNYLLSHSGLDYKRNILNDRNPVVTEDVEGDKKIYNAEVAE > WDKLRQRLLDARNKITSAESAVNSARNNLSARTNEQKHANDALNALLKEK > ENIRNQLSGINQKIAEEKRKQDELKATKDAINFTTEFLKSVSEKYGAKAE > QLAREMAGQAKGKKIRNVE-EALKTYEKYRADINKKINAKDRAAIAAALE > SVKLSDISSNLNRFSRGLGYAGKFTSLADWITEFGKAVRTENWRPLFVKT > ETIIAGNAATALVALVFSILTGSALGIIGYGLLMAVTGALIDESLVEKAN > KFW* > >P1;1mob > sequence:1mob > ------MSYMVARMQKMKAGNLGGAFKHNERVFETHSNKDINPSRSHLN- > --YELTDRDRSVSYEKQIKDYVNENKVSNRAIRKDAVLCDEWIITSDKD- > -----------FFEKLDEEQTRTFFETAKNYFAENYG-ESNIAYASVHLD > ESTPHMHMGVVPFENGKLSSKAMFDREELKHIQEDLPR--YMSDHGFELE > -------------------------------RGKLNSEAKHKTVAEFKRA > MADMELKEELLEKYHAPLFVDERTG--ELNNDTEAFWHEKEFADMFEVQS > PIRETTNQEKMDWLRKQYQEELKKLESSKKP-LEDDLSHLEELLDKKTKE > YIKIDSEASERASELSKAEGYINTLEN--HSKSLEAKIECLESDNLQLEK > Q----KATKLEAKALNES----ELRELKPKKNFLGKEHYELSPEQ---FE > GLKAEVYRSRTLLHHKDIELEQAKRQVSLRASKNYFTASLERAKEKAKGE > SIDR--LKSEIKRLKN------------E----N-SILRQQNDK-MLGKL > RELMPDKAFKNLLSELKAIKP-----------IVNIIKKAIEKSLF---- > ---* > > =====================MOB4.log================================= > MODELLER 6v2, 17 Feb 2002 > > PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS > > > Copyright(c) 1989-2002 Andrej Sali > All Rights Reserved > > Written by A. Sali > with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, > B. Jerkovic, A. Badretdinov, F. Melo, > J.P. Overington & E. Feyfant > Rockefeller University, New York, USA > Harvard University, Cambridge, USA > Imperial Cancer Research Fund, London, UK > Birkbeck College, University of London, London, UK > > Kind, OS, HostName, Kernel, Processor: 4, IRIX64 akilonia 6.5 IP30 > Date and time of compilation : 07/05/2002 17:12:26 > Job starting time (YY/MM/DD HH:MM:SS): 2003/03/21 23:47:53.033 > > TOP_________> 105 705 SET ALNFILE = 'MOB4.ali' > > TOP_________> 106 706 SET KNOWNS = '1cii' > > TOP_________> 107 707 SET SEQUENCE = '1mob' > > TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files' > > TOP_________> 109 709 SET STARTING_MODEL = 1 > > TOP_________> 110 710 SET ENDING_MODEL = 1 > > TOP_________> 111 711 CHECK_ALIGNMENT > > check_a_343_> >> BEGINNING OF COMMAND > check_a_335E> No alignment. > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Dynamically allocated memory at finish [B,kB,MB]: 2200483 > 2148.909 2.099 > Starting time : 2003/03/21 > 23:47:53.033 > Closing time : 2003/03/21 > 23:48:02.202 > Total CPU time [seconds] : 0.00 > > ------ End of Forwarded Message
-
Andrej Sali -
Difei Wang -
Luca Settimo -
Margot Ernst -
Modeller Care -
Stephane Vandevuer