Subject: Re: Bad template?--log ali. and top files.
From: Lei Wang <>
Date: Thu, 02 May 2002 15:25:39 -0400
Cc:
log file:
#######################################
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, Linux master.cl.mssm.edu
2.4.9-13smp i686
Date and time of compilation : 01/24/2002 16:28:15
Job starting time (YY/MM/DD HH:MM:SS): 2002/05/02 11:04:08.230
getprog_531W> ROUTINE redefined: getnames
check_ali___> Checking the sequence-structure alignment.
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
############################################
Top file:
*********************************
INCLUDE
SET ATOM_FILES_DIRECTORY = './'
SET ALNFILE = '1gh0B-3-1eyxK.ali'
SET KNOWNS = '1eyxK'
SET SEQUENCE = '1gh0B'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 5
CALL ROUTINE = 'model'
SUBROUTINE ROUTINE = 'getnames'
STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION = 'EQ', THEN =
;
'STRING_OPERATE OPERATION = CONCATENATE, STRING_ARGUMENTS =
1gh0B-3-1eyxK .ini, RESULT = MODEL'
STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATION = 'EQ', THEN
= ;
'STRING_OPERATE OPERATION = CONCATENATE, STRING_ARGUMENTS =
1gh0B-3-1eyxK .rsr, RESULT = CSRFILE'
STRING_OPERATE OPERATION = 'CONCATENATE', ;
STRING_ARGUMENTS = '1gh0B-3-1eyxK' '.sch', RESULT = SCHFILE
STRING_OPERATE OPERATION = 'CONCATENATE', ;
STRING_ARGUMENTS = '1gh0B-3-1eyxK' '.mat', RESULT = MATRIX_FILE
SET ROOT_NAME = '1gh0B-3-1eyxK'
RETURN
END_SUBROUTINE
*************************************
>P1;1gh0B
structureX:1gh0B: 1 :B: 172 :B:undefined:undefined:-1.00:-1.00
MFDAFTKVVSQADTRGEMLSTAQIDALSQMVAESNKRLDVVNRITSNASTIVSNAARSLFAEQPQLIAPGG-AYT
SRRMAACLRDMEIILRYVTYAVFAGDASVLEDRCLNGLRETYLALGTPGSSVAVGVGKMKEAALA---IVNDPAG
ITPGDCSALASEIAGYFDRAAAAVS*
>P1;1eyxK
structureX:1eyxK: 1 : : 164 : :undefined:undefined:-1.00:-1.00
MKSVITTVISAADSAGRFPSSSDLESVQGNIQRASARLEAAEKLASNHEAVVKEAGDACFGKYGYLKNPGEAGEN
QEKINKCYRDIDHYMRLVNYSLVIGGTGPLDEWGIAGAREVYRTLNLPTSAYIAAFAFTRDR-LCGPRDMS----
-----AQ-AGVEYSTALDYIINSLS*
--- Begin Message ---
To:
From: Lei Wang <>
Date: Wed, 01 May 2002 23:16:10 -0400
Priority: normal
Dear Modellers,
I'm trying to build models with 1eyxK as template, and always fails.
The error message I get:
MODELLER stopped with message : /usr/local/bio/modeller6v1/bin/mod6v1:
line 41: 32686 Segmentation fault
$NICE ${EXECUTABLE} $STEERF >$LOGF
***************************************
What kind of error could this be? Are there any reason that 1eyxK is a
bad template to use?
Any input is appreciated,
Lei