[modeller_usage] Some tutorial issues

[Michael Mayhew <>]

Greetings,

   I am using python2.5.1 and modeller version 9v3 on a Mac desktop 
(OSX 10.4.8).

   I saw a similar post in the discussion board regarding the 
compare.py script of the tutorial where the function call generated an 
error message. However, the information therein didn't really help me.

   I also referred to the user manual and found that in my version of 
modeller, malign_3d has been deprecated and that I should use salign. 
However, salign (in the context of the tutorial exercise) does not 
return an object that can be used to continue the tutorial.

   I am running the compare.py script from a directory on my Desktop 
separate from the modeller installation directory (should I be running 
the script from within the modeller directory?)

   For posterity, I have included my 'version' of the compare.py script 
and the error message from the python interpreter.
  
   Thanks for your time and consideration in this matter.

Michael Mayhew


<<< compare.py >>>

from modeller import *

env = environ()
aln = alignment(env, file='pdball.pir',
               align_codes=('1b8pA', '1bdmA', '1civA', '5mdhA', 
'7mdhA', '1smkA'))

aln. malign()
aln.malign3d()
aln.compare_structures()
aln.id_table(matrix_file='family.mat')
env.dendogram(matrix_file='family.mat', cluster_cut=-1.0)

<<< python traceback error message >>>

Multiple dynamic programming alignment (MALIGN):
 Residue-residue metric  : $(LIB)/as1.sim.mat
 ALIGN_BLOCK             :            1
 Gap introduction penalty:    -900.0000
 Gap extension penalty   :     -50.0000
 Length of alignment     :          384
pdbnam_____E> Filename for PDB code not found: 1b8p
             Directories:
             Extensions : :.atm:.pdb:.ent:.crd
             (Also tried prepending 'pdb', and looking for .Z, .gz, .bz2)

Traceback (most recent call last):
 File "compare.py", line 8, in <module>
   aln.malign3d()
 File "/Library/modeller-9v3/modlib/modeller/alignment.py", line 295, 
in malign3d
   edit_file_ext)
IOError: pdbnam_____E> Filename for PDB code not found: 1b8p
             Directories:
             Extensions : :.atm:.pdb:.ent:.crd
             (Also tried prepending 'pdb', and looking for .Z, .gz, .bz2)