SSIPe Error - Protein Chains

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SSIPe Error - Protein Chains

Post by whitejaa »

I am trying to use SSIPe; however, I get an error when I run the software at the website. I get the following error, “ERROR! Invalid complex structures. SSIPe requires two chains in the input complex structure, but 1 chain is detected in the PDB file." I used Phyre2 to generate my pdb and when I examine it I do not see any chain identifiers. Is there a way for me to fix this error? Thanks!
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Joined: Tue May 04, 2021 5:05 pm

Re: SSIPe Error - Protein Chains

Post by xiaoqiah »


Thanks for using the SSIPe service.

You encountered this error because your pdb was identified as a monomer (single-chain protein) by the SSIPe server. Based on your description, this was probably because your pdb does not have the chain identifier(s). I suggest you do:

(1) check if your protein model by Phyre2 is a dimer. If it is a monomer, you may get the wrong model in this step.
(2) If you make sure that your model is dimer, you can directly add chain identifiers by yourself using a text editor such as UltraEdit or Notepad++. Or if you are familiar with script languages, you can write scripts to do the same thing.

Or you can contact me at, I would like to help you check what is going on with your pdb files.

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