SSIPe Error - Protein Chains
Moderator: robpearc
SSIPe Error - Protein Chains
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!
Re: SSIPe Error - Protein Chains
Hello,
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 xiaoqiah@umich.edu, I would like to help you check what is going on with your pdb files.
Xiaoqiang,
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 xiaoqiah@umich.edu, I would like to help you check what is going on with your pdb files.
Xiaoqiang,