Error In Modeller
Hello all i am running modeller9.11 using mod9.11 script[...] using my script ....on which it is giving import site error import site failed: use -v for traceback what is the meaning of this error and how to solve it ?
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Can you post your script which gave this error and copy the full error output? It looks like you didn't install one of the files that you are trying to import, but it's impossible to say without seeing the script.
from modeller import *
log.verbose() env = environ()
#-- Prepare the input files
#-- Read in the sequence database sdb = sequence_db(env) sdb.read(seq_database_file='pdb_95.pir', seq_database_format='PIR', chains_list='ALL', minmax_db_seq_len=(30, 4000), clean_sequences=True)
#-- Write the sequence database in binary form sdb.write(seq_database_file='pdb_95.bin', seq_database_format='BINARY', chains_list='ALL')
#-- Now, read in the binary database sdb.read(seq_database_file='pdb_95.bin', seq_database_format='BINARY', chains_list='ALL') #-- Read in the target sequence/alignment aln = alignment(env) aln.append(file='qseq1.ali', alignment_format='PIR', align_codes='ALL') #-- Convert the input sequence/alignment into
profile format
prf = aln.to_profile() #-- Scan sequence database to pick up homologous sequences prf.build(sdb, matrix_offset=-450, rr_file='${LIB}/blosum62.sim.mat', gap_penalties_1d=(-500, -50), n_prof_iterations=1, check_profile=False, max_aln_evalue=0.01) #-- Write out the profile in text format prf.write(file='build_profile.prf', profile_format='TEXT') #-- Convert the profile back to alignment format aln = prf.to_alignment() #-- Write out the alignment file aln.write(file='build_profile.ali', alignment_format='PIR')
And the full error when you use the -v option?
C:\Program Files (x86)\Modeller9.10> mod9v1 is not recongnized as an internal and external command, operable program or batch file."
It means the MODELLER bin directory is not in your PATH. Did you move the installation directory?