matziast@med.uth.gr wrote:
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 (('1b8p', 'A'), ('1bdm', 'A'), ('1civ', 'A'),
('5mdh', 'A'), ('7mdh', 'A'), ('1smk', '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.
...
IOError: pdbnam_____E> Filename for PDB code not found: 1b8p
You are trying to do a structural comparison of several structures. Obviously, in order to do that you need the structures (PDB files). Looks like you don't have any of them, because Modeller is complaining that it can't find the first one (1b8p). This will usually be called something like 1b8p.pdb or pdb1b8p.ent. As described in the basic modeling tutorial, you need to either download the structures from PDB or get them from the archive (.zip or .tar.gz file) linked at the top of the basic modeling tutorial webpage.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage