KeyError: ‘subject-id’ in antibody modelling

[Anonymous]

Dear all,

I have recently started learning Rosetta. Now I am working on antibody modelling. I have prepared my inputs, have blast and Pro-Fit working.  When I am running the antibody.py with the default preprocessing options

/home/bogac/softwares/rosetta/rosetta_bin_linux_2016.32.58837_bundle/tools/antibody/antibody.py --light-chain light_chain.fasta --heavy-chain heavy_chain.fasta

--superimpose-profit=/home/bogac/softwares/profit/ProFitV3.1/profit

--blast=/home/bogac/softwares/blast/ncbi-blast-2.6.0+-src/c++/ReleaseMT/bin/blastp

--blast-database=/home/bogac/softwares/rosetta/rosetta_bin_linux_2016.32.58837_bundle/tools/antibody/blast_database

--antibody-database=/home/bogac/softwares/rosetta/rosetta_bin_linux_2016.32.58837_bundle/tools/antibody/antibody_database

--rosetta-bin=/home/bogac/softwares/rosetta/rosetta_bin_linux_2016.32.58837_bundle/main/source/bin

--rosetta-database=/home/bogac/softwares/rosetta/rosetta_bin_linux_2016.32.58837_bundle/main/database --rosetta-platform=static.linuxgccrelease

I am having the following error, when pblast starts to run;

Running /home/bogac/softwares/blast/ncbi-blast-2.6.0+-src/c++/ReleaseMT/bin/blastp

I: Queryname=FRL

I: Found 600 blast results (limit 600)

Traceback (most recent call last):

File "/home/bogac/softwares/rosetta/rosetta_bin_linux_2016.32.58837_bundle/tools/antibody/antibody.py", line 1640, in <module>

if __name__ == "__main__": main(sys.argv)

File "/home/bogac/softwares/rosetta/rosetta_bin_linux_2016.32.58837_bundle/tools/antibody/antibody.py", line 400, in main

alignment, legend = run_blast(CDRs, prefix=prefix_details, blast=Options.blast, blast_database=Options.blast_database, verbose=Options.verbose)

File "/home/bogac/softwares/rosetta/rosetta_bin_linux_2016.32.58837_bundle/tools/antibody/antibody.py", line 990, in run_blast

f(k, table, cdr_query, cdr_info)

File "/home/bogac/softwares/rosetta/rosetta_bin_linux_2016.32.58837_bundle/tools/antibody/antibody.py", line 1465, in filter_by_template_resolution

pdb = r

KeyError: 'subject-id'

 

Can anybody please guide me how solve this problem ?

Thank you very much for your help. Kind regards

 

Bogac

[Anonymous]

Bogac,

Your error is due to BLAST changing the output header from “subject-id” to “subject-acc.ver”, so a simple fix is to alter line 1465 in the Python code to use the new header. But, the python version of antibody modeling is out dated and I would advise using the latest C++ version (a detailed write-up can be found here). 

-Jeliazko

[Anonymous]

Bogac,

Your error is due to BLAST changing the output header from “subject-id” to “subject-acc.ver”, so a simple fix is to alter line 1465 in the Python code to use the new header. But, the python version of antibody modeling is out dated and I would advise using the latest C++ version (a detailed write-up can be found here). 

-Jeliazko

[Anonymous]

Bogac,

Your error is due to BLAST changing the output header from “subject-id” to “subject-acc.ver”, so a simple fix is to alter line 1465 in the Python code to use the new header. But, the python version of antibody modeling is out dated and I would advise using the latest C++ version (a detailed write-up can be found here). 

-Jeliazko

[Anonymous]

Dear Jeliazko,

 

Thank you very much for the update. I will be following your advice and the paper.

 

Kind regards

Bogac

[Anonymous]

Dear Jeliazko,

 

Thank you very much for the update. I will be following your advice and the paper.

 

Kind regards

Bogac

[Anonymous]

Dear Jeliazko,

 

Thank you very much for the update. I will be following your advice and the paper.

 

Kind regards

Bogac

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