Expresso failed, X-ray and NMR structure templates?

[KamillaOJ]

Hi! 

Im having trouble with T-Coffee Expresso through the webserver. I used the sequences extracted from PDB (from CATH database). I had some errors, I think because no structural templates where found ( http://tcoffee.crg.cat/apps/tcoffee/result?rid=46a0b0ec ) so I have uploaded a list of templates to be used for each sequences. It still failed ( http://tcoffee.crg.cat/apps/tcoffee/result?rid=6f4f9311 ), but I think the issue is that only X-ray PDBs are used. I don't see an option to change to both X-ray and NMR templates, but I found in the protocol that it should be possible with the argument -pdb_type dn.

Is it possible to use both NMR and Xray structure template in the webserver ? Can it be another reason why my alignment failed?

Kind Regards, Kamilla

[athbaltzis]

Hi Kamilla,

Yes, you could do the following:
In the homepage of the webserver you can scroll down to select the option "Advanced" under the section "Other". Then, you can upload your files (input fasta, pdb files and your template file) and in the second step you can write the following command:

-in=all_PHS60_m8.fasta -mode=3dcoffee -blast=LOCAL -pdb_db=/db/pdb/derived_data_format/blast/latest/pdb_seqres.fa -pdb_type=dn -template_file -evaluate_mode=t_coffee_slow -output=score_html clustalw_aln fasta_aln score_ascii phylip -maxnseq=150 -maxlen=2500 -case=upper -seqnos=off -outorder=input -run_name=result -multi_core=4 -quiet=stdout

Here you can find an example of a template file https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html#using-3d-structures-expresso-3d-coffee

Best,
Athanasios

[KamillaOJ]

Thank you. I tried, but it failed again after 2h 59m. Im not sure why, and there was no error file this time.

http://tcoffee.crg.cat/apps/tcoffee/result?rid=ae25ee57

I uploaded fasta sequences and the template file.

Best,
Kamilla

[cnotred]

Hi Kamilla, Your dataset is largish for 3D-Coffee. This may be the issue. Can you send us the dataset so we look at it. Please send it dirctly to me or Athanasio Cheers, Cedric Le 8/4/21 à 11:16, Kamilla Ormevik Jansen a écrit :

Thank you. I tried, but it failed again after 2h 59m. Im not sure why, and there was no error file this time. http://tcoffee.crg.cat/apps/tcoffee/result?rid=ae25ee57 <http://tcoffee.crg.cat/apps/tcoffee/result?rid=ae25ee57> I uploaded fasta sequences and the template file. Best, Kamilla — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#41 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABML3KP6MH4NPBTMCW5EE2DTHVX5VANCNFSM42QGN44Q>.

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