[modeller_usage] error when trying to set MDT_LIB_FILE and BIN_LIB_FILE

[Daniel Rigden <>]

Dear all

I sometimes need to reconstruct a complete structure from a main chain
alone structure derived from dynamic analysis.  To do this I have, in
the past, used a modified mkhomcsr routine to take main chain
constraints from one structure (the main chain alone) and side chain
constraints from another (the original crystal structure).  In the past
this has worked.  Now, for some reason, on a different machine but
running the same v6.2 of modeller, I get errors.

My remodelled routine looks like this

---------------------------------------------
SUBROUTINE ROUTINE = 'mkhomcsr'

SET MAX_CA-CA_DISTANCE = 30.0
SET MAX_N-O_DISTANCE   = 20.0
SET MAX_SC-MC_DISTANCE =  4.5
SET MAX_SC-SC_DISTANCE =  6.0

MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo', ADD_RESTRAINTS = OFF

### MNCH restraints!
READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES =  'mc_only' SEQUENCE
SET MDT_LIB_FILE  = '${LIB}/mnch1.mdt'
SET BIN_LIB_FILE  = '${LIB}/mnch1.bin'
MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_RESTRAINTS = ON

etc.
---------------------------------------------

but MODELLER gives errors of this type

---------------------------------------------
getprog_531W> ROUTINE redefined:  mkhomcsr
assgn___544E> Variable name not recognized:  MDT_LIB_FILE
              Command line:  SET MDT_LIB_FILE  = '${LIB}/mnch1.mdt'
assgn___525E> Error in TOP variable assignment.
assgn___544E> Variable name not recognized:  BIN_LIB_FILE
              Command line:  SET BIN_LIB_FILE  = '${LIB}/mnch1.bin'

etc.
---------------------------------------------

Can anyone tell me why Modeller isn't recognising these variable names?
It's not a general issue - simpler modelling tasks run fine.

Many thanks in advance

Daniel

-- 
Dr Daniel John Rigden                     Tel:(+44) 151 795 4467
School of Biological Sciences             FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool
Crown St.,
Liverpool L69 7ZB, U.K.