Antibody modeling

[Anonymous]

Hello,

I am using Rosetta 15.31 for antibody modeling. when I run the following command:

./antibody.py –light-chain Cer.VL.Seq.fasta –heavy-chain Cer.VH.seq.fasta –superimpose_profit /home/mary/antibody-modeling/ProFitV3.1
–blast /home/mary/antibody-modeling/ncbi-blast-2.2.30+/bin –blast-database /home/mary/antibody-modeling/rosetta/tools/antibody/blast_database
–antibody-database /home/mary/antibody-modeling/rosetta/tools/antibody/antibody_database –rosetta-bin /home/mary/antibody-modeling/rosetta /main/source/bin –rosetta-database /home/mary/antibody-modeling/rosetta15-12/main/database –rosetta-platform /home/mary/antibody-modeling/rosetta/main/source/bin

then, I faced with the following error:

Preparing cter_constraint file for H3 modeling
H3: 9 GYRSYAMDY
Key residues: TYR ALA TYR ALA ARG ALA MET ASP
Predicted base conformation is KINK
./kink_constraints.py grafting//model.pdb
ERROR making constraint file: 256
Traceback (most recent call last):
File “./kink_constraints.py”, line 5, in
from rosetta import *

ImportError: No module named rosetta

I have no idea what this error means. What can I do to fix this?

[Anonymous]

The kink_constraints.py script requires that PyRosetta also be installed on your machine, for the same version of Python that you’re using to run the antibody.py script.

[Anonymous]

I installed PyRosetta.Ubuntu-12.04LTS.64Bit.devel-r56795, and run the antibody modeling command: 

./antibody.py –light-chain Cer.VL.Seq.fasta –heavy-chain Cer.VH.seq.fasta –superimpose_profit /home/mary/antibody-modeling/ProFitV3.1

–blast /home/mary/antibody-modeling/ncbi-blast-2.2.30+/bin –blast-database /home/mary/antibody-modeling/rosetta/tools/antibody/blast_database

–antibody-database /home/mary/antibody-modeling/rosetta/tools/antibody/antibody_database –rosetta-bin /home/mary/antibody-modeling/rosetta /main/source/bin –rosetta-database /home/mary/antibody-modeling/rosetta15-12/main/database –rosetta-platform /home/mary/antibody-modeling/rosetta/main/source/bin

but I faced with the following error: 

Error2: ./kink_constraints.py grafting//model.pdb

ERROR making constraint file: 256

Traceback (most recent call last):

  File “./kink_constraints.py”, line 5, in <module>

    from rosetta import *

  File “/home/hamzeh/biomed/PyRosetta.Ubuntu-12.04LTS.64Bit.devel-r56795/rosetta/__init__.py”, line 45, in <module>

    import numeric

ImportError: No module named numeric

what should i do with the error?

[Anonymous]

Many thanks for your help.

[Anonymous]

In order to run PyRosetta, you need to have your environment set up appropriately. Normally this takes the form of running “source SetPyRosettaEnvironment.sh” in your (bash) commandline prior to using PyRosetta. You can find the SetPyRosettaEnvironment.sh in the PyRosetta directory.

(What this does is set the PYHONPATH environment variable to include the directories where the PyRosetta libraries are located, so when you do things like “import numeric”, Python knows were to find the numeric library from PyRosetta.)

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