[modeller_usage] malign3d will not align multiple structures

[Mark Daniels <>]

Hello all-

  I'm trying to run malign3d to align multiple models but the routine 
only 'sees' the first structure and does nothing.  I'm using the 
malign3d.top file format described in the Sanchez and Sali 2000 Methods 
in Molecular Biology article:

SET OUTPUT_CONTROL = 1 1 1 1 2
SET MAXRES = 700
SET ATOM_FILES = 'atip.B99990001'  'atip.B99990002'  ;
'atip.B99990003'  'atip.B99990004'  'atip.B99990005'
SET WRITE_FIT = on
MALIGN3D

All the atip.Bxxxx files contain a reasonable structure.  Running the 
malign3d.top routine shown above fails to produce any .fit files and 
shows the following error:

openf5__224_> Open       11  OLD  SEQUENTIAL  atip.B99990001
malign3_327W> Only one structure; nothing done.

Would anyone be able to advise me on what I'm missing here or doing 
wrong?

Thanks in advance-

Mark Daniels
The Scripps Research Institute