[modeller_usage] CHECK_ALIGNMENT accepts it, but ROUTINE = 'model' does not.
To:
Subject: [modeller_usage] CHECK_ALIGNMENT accepts it, but ROUTINE = 'model' does not.
From: Javier Satulovsky <>
Date: Tue, 08 Jun 2004 14:52:27 -0700
Hi,
I'm learning how to use modeller (release 6 with linux red hat 9).
While CHECK_ALIGNMENT seems accept my alignment, calling the
routine 'model' gives me an error when trying to read that same
alignment.
I 'm trying to model 41 residues into the first chain of the PDB file
1GL2.pdb (after this 'practice run' I will try to model the four chains
of the
structure at the same time).
Following are relevant parts of scripts+logs.
Any ideas will be greatly appreciated!!!
Javier.
modeller.alignment.ali
----------------------
chech_alignment.log (last part of the file)
-------------------
openf5__224_> Open 11 OLD SEQUENTIAL modeller.alignment.ali
Read the alignment from file : modeller.alignment.ali
Total number of alignment positions: 41
# Code #_Res #_Segm PDB_code Name
1 1GL2 A 41 1 1GL2 Endobrevin
2 1GGX 41 1 1GGX ykt6
TOP_________> 4 4 WRITE_ALIGNMENT FILE = 'alignment.ali'
openf5__224_> Open 14 UNKNOWN SEQUENTIAL alignment.ali
TOP_________> 5 5 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND
openf5__224_> Open 11 OLD SEQUENTIAL ./../atom_files/1GL2.atm
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
check_a_344_> << END OF COMMAND
Dynamically allocated memory at finish [B,kB,MB]:
3061621 2989.864 2.920
Starting time : 2004/06/08
16:10:06.379
Closing time : 2004/06/08
16:10:13.541
Total CPU time [seconds] : 3.47
modelling.top
-------------
INCLUDE
SET OUTPUT_CONTROL = 1 1 1 1 1
SET ALNFILE = './alignment.ali'
SET KNOWNS = '1GL2'
SET SEQUENCE = '1GGX'
SET ATOM_FILES_DIRECTORY = '../atom_files'
SET STARTING_MODEL= 1
SET ENDING_MODEL = 1
CALL ROUTINE = 'model'
modelling.log (last part of the file)
-------------
TOP_________> 111 711 CALL ROUTINE = 'model'
TOP_________> 112 399 CALL ROUTINE = 'getnames'
TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL
'undefined', OPERATION;
= 'EQ', THEN = 'STRING_OPERATE OPERATION =
CONCATENA;
TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT =
MODEL'
TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE
'undefined', OPERATI;
ON = 'EQ', THEN = 'STRING_OPERATE OPERATION =
CONCATE;
NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT =
CSRFILE;