Multiple Template Alignment Problems - MAXRES

[Alex Brown <>]

Hi.

At the moment, i am going through the examples found in 'Comparative 
Protein Structure Modeling. Introductionand Practical Examples with 
Modeller' from the Methods in Molecular Biology Series. Everything 
seemed to be o.k., until I started the third section - using multiple 
templates:

Using the following TOP script:

SET OUTPUT_CONTROL = 1 1 1 1 1
SET ALIGN_CODES = '1hms' '1lid'
SET ATOM_FILES = '1hms.pdb' '1lid.pdb'
MALIGN3D
SET ADD_SEQUENCE = on, ALIGN_BLOCK = NUMB_OF_SEQUENCES
READ_ALIGNMENT FILE = 'blbp.seq', ALIGN_CODES = ALIGN_CODES 'blbp'
ALIGN2D
WRITE_ALIGNMENT FILE = 'blbp-1hms-1lid.ali', ALIGNMENT_FORMAT = 'PIR'
WRITE_ALIGNMENT FILE = 'blbp-1hms-1lid.pap', ALIGNMENT_FORMAT = 'PAP'

I get the following error reports in the .log file:

Dynamically allocated memory at         amaxseq [B,kB,MB]:      
2200483    2148.909     2.099
TOP_________>     2    2 SET ALIGN_CODES = '1hms' '1lid'


Dynamically allocated memory at         amaxseq [B,kB,MB]:      
2205269    2153.583     2.103
TOP_________>     3    3 SET ATOM_FILES = '1hms.pdb' '1lid.pdb'

TOP_________>     4    4 MALIGN3D


Dynamically allocated memory at         amaxbnd [B,kB,MB]:      
2560929    2500.907     2.442
openf5__224_> Open       11  OLD  SEQUENTIAL  1hms.pdb
rdpdb___223E> Array too small. Increase  MAXRES
              current maximum, current need:       30       31
rdabrk__288W> Protein not accepted:        1
rdabrk__291E> Sequence difference between alignment and  pdb :

   STRUCTURE RES_IND  ALN_ITYP  ALN_RES  X_ITYP  X_RES  -----*-----
           1       1        33     GLYP       0         -----######
rdabrk__288W> Protein not accepted:        1
openf5__224_> Open       11  OLD  SEQUENTIAL  1lid.pdb
rdpdb___223E> Array too small. Increase  MAXRES
              current maximum, current need:       30       31
rdabrk__288W> Protein not accepted:        2
rdabrk__291E> Sequence difference between alignment and  pdb :

   STRUCTURE RES_IND  ALN_ITYP  ALN_RES  X_ITYP  X_RES  -----*-----
           2       1        33     GLYP       0         -----######
rdabrk__288W> Protein not accepted:        2
fndatmi_285W> Number of residues <> number of atoms; atom code:       
31        0  CA
fndatmi_284E> Beginning atom index for a residue out of bounds:        
0      237
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Why won't MODELLER read the template sequences, and how do I increase 
the MAXRES variable.

I am running MODELLER6v2 on Darwin (Mac OSX).

Many Thanks,

Alex Brown.