The installation looks good, the program runs. As a first attempt, please try to run examples from the examples/ directory of the distribution package and please look into the files for details.

1xnb is not found in your pir sequence file, and indeed you have 1fdx.

If you want to run a sequence search, you need to specify a few more environment variables that will point Modeller to the respective databses. For details please see the manual: http://salilab.org/modeller/manual/node14.html and comments in the example top files. Andras

vuissoz Jean-Marc wrote: > > dear modeller team, > Probably something is not installed correctly on my version of modeller6.1 > but I don't find what, > here are the log files en top files with the error reported. > best tanks > > vuissoz jean-marc > >P1;1fdx > sequence:1fdx:1 : :54 : :ferredoxin:Peptococcus aerogenes: > >2.00:-1.00 > AYVINDSCIACGECPVNIIQGSIYAIDADSCIDCGSCASVCPVGAPNPED* > > SET SEARCH_RANDOMIZATIONS = 100 > SET FILE = 'prot.ali' > SEQUENCE_SEARCH > ALIGN_CODES = '1fdx', DATA_FILE = ON > > MODELLER 6v1, 17 Jan 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 IRIS 6.5 > IP30 > Date and time of compilation : 01/25/2002 20:36:35 > Job > starting time (YY/MM/DD HH:MM:SS): 2002/02/15 17:44:24.629 > > read_se_367E> > Sequence not found; code: P1;1xnb > recover____E> ERROR_STATUS >= > STOP_ON_ERROR: 1 1 > > Dynamically allocated memory at > finish [B,kB,MB]: 2306323 2252.269 2.199 > Starting time > : 2002/02/15 17:44:24.629 > Closing time > : 2002/02/15 17:44:33.146 > Total CPU time [seconds] > : 0.00

Hi everybody,

There was a problem with MODELLER CHAINS files (found in /modlib directory). Problem has been solved and new version of MODELLER 6v1 placed on the web.

This affects you only if you are using MODELLER to search for the templates.

Thanks, Bozidar

-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of vuissoz Jean-Marc Sent: Saturday, February 16, 2002 10:48 AM To: modeller_usage@salilab.org Subject: bug report

dear modeller team, Probably something is not installed correctly on my version of modeller6.1 but I don't find what, here are the log files en top files with the error reported. best tanks

vuissoz jean-marc >P1;1fdx sequence:1fdx:1 : :54 : :ferredoxin:Peptococcus aerogenes: >2.00:-1.00 AYVINDSCIACGECPVNIIQGSIYAIDADSCIDCGSCASVCPVGAPNPED*

SET SEARCH_RANDOMIZATIONS = 100 SET FILE = 'prot.ali' SEQUENCE_SEARCH ALIGN_CODES = '1fdx', DATA_FILE = ON

MODELLER 6v1, 17 Jan 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 IRIS 6.5 IP30 Date and time of compilation : 01/25/2002 20:36:35 Job starting time (YY/MM/DD HH:MM:SS): 2002/02/15 17:44:24.629

read_se_367E> Sequence not found; code: P1;1xnb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

Dynamically allocated memory at finish [B,kB,MB]: 2306323 2252.269 2.199 Starting time : 2002/02/15 17:44:24.629 Closing time : 2002/02/15 17:44:33.146 Total CPU time [seconds] : 0.00