[modeller_usage] CHECK_ALIGNMENT accepts it, but ROUTINE = 'model' does not.

[Javier Satulovsky <satulovsky AT mailblocks.com>]

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
----------------------
> >P1;1GL2
> structureX:1GL2:20:A:60:A:Endobrevin:rattus norvegicus:1.9:0.1370
> EGVKNIMTQNVERILARGENLDHLRNKTEDLEATSEHFKTT
> *
>
> >P1;1GGX
> sequence:1GGX:1: :41: :ykt6:rattus norvegicus::
> DETKIILHNTMESLLERGEKLDDLVSKSEVLGTQSKAFYKT
> *

chech_alignment.top
-------------------
> SET OUTPUT_CONTROL = 1 1 1 1 1
> SET ATOM_FILES_DIRECTORY = './../atom_files'
>
> READ_ALIGNMENT FILE = 'modeller.alignment.ali', ALIGN_CODES = 'all'
> WRITE_ALIGNMENT FILE = 'alignment.ali'
> CHECK_ALIGNMENT
	

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;
                     '

TOP_________>   115  511 STRING_OPERATE OPERATION = 'CONCATENATE',      
         ;
                         STRING_ARGUMENTS = SEQUENCE '.sch',  RESULT = 
SCHFILE

TOP_________>   116  512 STRING_OPERATE OPERATION = 'CONCATENATE',      
         ;
                        STRING_ARGUMENTS = SEQUENCE '.mat',  RESULT = 
MATRIX_FI;
                     LE

TOP_________>   117  513 SET ROOT_NAME = SEQUENCE

TOP_________>   118  514 RETURN

TOP_________>   119  400 CALL ROUTINE = 'homcsr'

TOP_________>   120  106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = 
KNOWNS SEQUE;
                     NCE


Dynamically allocated memory at         amaxseq [B,kB,MB]:      2205269 
  2153.583     2.103
openf5__224_> Open       11  OLD  SEQUENTIAL  ./alignment.ali

Dynamically allocated memory at         amaxbnd [B,kB,MB]:      3061621 
  2989.864     2.920
openf5__224_> Open       11  OLD  SEQUENTIAL  ./alignment.ali
read_al_375E> Unknown residue type,position,sequence:          1        
1
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Dynamically allocated memory at          finish [B,kB,MB]:      3061621 
  2989.864     2.920
Starting time                                            : 2004/06/08  
16:07:55.650
Closing time                                             : 2004/06/08  
16:08:04.684
Total CPU time [seconds]                                 :       4.30


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