While I was running the second script which is called compare.py and is the
following:
from modeller import *
env = Environ()
aln = Alignment(env)
for (pdb, chain) in (('1jfw', 'A'), ('4ogr', 'D'), ('4or5', 'C'),
('3o6l', 'C'), ('3mi9', 'C'), ('1tbc', 'A'), ('1tiv', 'A')):
m = Model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain))
aln.append_model(m, atom_files=pdb, align_codes=pdb+chain)
aln.malign()
aln.malign3d()
aln.compare_structures()
aln.id_table(matrix_file='family.mat')
env.dendrogram(matrix_file='family.mat', cluster_cut=-1.0)
I recieved the following message and I don't know what to do.
You can find many useful example scripts in the
examples\automodel directory.
It is recommended that you use Python to run
Modeller scripts. However, if you don't have Python installed,
you can type 'mod10.5' to run them instead.
C:\Program Files\Modeller10.5>cd bin
C:\Program Files\Modeller10.5\bin>cd Modeller_test
C:\Program Files\Modeller10.5\bin\Modeller_test>mod10.5 compare.py
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "compare.py", line 10, in ?
aln.malign3d()
File "C:\Program Files\Modeller10.5\modlib\modeller\alignment.py", line 348, in malign3d
edit_file_ext)
_modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 0
Please, help me.