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.