Issues with CPORT

Good morning!

I ran PDB structures back in February and the output seemed fine - there was a list of active/passive residues, and most predictors worked.

Tried running the same PDB structures this week - nothing appears under the section of active/passive residues and majority of the predictors failed.

Can I please have some help? Thank you!

Did you try again?

Note that our WHISCY server, which is called by CPORT has been migrated to a new server / frontend.
Because of that CPORT can currently not query it anymore. But you can try to run WHISCY perditions directly.


Yes, I did. This is how the output looked like in February.

And with the same PDB structure, this is the output I’ve gotten this week. I’ve ran it thrice.

Since we depend on external servers it is not something we really have under our control

CPORT is already quite old, so are some of the servers it queries.

Did you try our WHISCY portal?

Hi, I apologize for the really long delay!
I’ve tried inputting my PDB file and the multiple sequence alignment in FASTA format (retrieved from Clustal Omega, with the first query sequence being the reference protein, and second query sequence being the modeled protein).

Initially, the PDB file had no chain ID. I’ve assigned it as Chain A on PyMol.

The failed output shows that a conservation file is missing, but I’m not sure how to go about this. Can you please advise me?

Dear @nurzabidi
After checking your issue carefully, we discovered a small problem on the sequence alignment processing. Nevertheless, we have fixed it, but still WHISCY server is not providing a prediction for your input data. Our guess is this provided MSA file is not sufficient (it only contains two sequences, one is actually the master one) to compute a reliable WHISCY prediction. Please try again providing more sequences in the MSA alignment file.

Hi Brian, thank you for your help! So, I realized that I made a careless mistake. After homology modeling, I didn’t assign a chain to my protein models. :woman_facepalming: After doing that, CPORT was able to come up with the predictions.

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Thank you for the feedback! Let us know if you experience any other problem regarding CPORT or WHISCY.

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Hi @bjimenez,

I’ve submitted a few jobs in CPORT, but I realized that the predictors no longer include WHISCY. Has the predictor been officially separated from CPORT?

Should there be any failed predictors (and the original server does not work manually - site does not even load), are there any suggestions of what can be done? In this case, it was specifically PIER across all jobs.

Looking forward to your reply, thank you!

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We do have a new version of the WHISCY server at:

But CPORT is indeed no longer accessing it. We are working on updating CPORT.

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