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Stepwise error

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Stepwise error

I am getting the following error while trying to assemble a 514-nucleotide long RNA using the "Stepwise" programme:

"one of your input pdbs -- native, alignment, or starting -- has a residue that is not found in the fasta!"

I have thoroughly checked my target fasta sequence  and the input PDB containing part of the RNA structure. There are no residue mismatches...then why am I getting this error?

Moreover when I am uploading three different PDBs containing parts of the target RNA, it is showing that my PDBs have overlapping residues. Which is not true again.

I am unable to attach the PDBs since they are exceeding the size limit allowed here.


Post Situation: 
Wed, 2021-10-06 08:57

While I'm not familiar with the specific scheme you are trying to run, I have encountered issues with other rosetta protocols where the problem was with mismatched numbering.

Rosetta really likes it when PDB residue numbers start from 1, especially when comparing to other PDBs.

I would suggest trying to make sure that the fasta sequence (since it has no numbering, it will be numbered 1-514) and the PDB files have consistent numbering of the residues in question.

And if you are using multiple PDB files, ensure that their numbering is not overlapping (so if one PDB is used to describe residues 1-200 from the fasta, and the other one shows 201-514, then the residue numbers in the PDB probably shouldnt both start from 1.)

I hope this helps, and if not, sorry for the confusion!

Thu, 2021-10-07 02:48

Thank you for the suggestion.

I renumbered the residues in the input PDBs ( I have three of them aligning to three different regions of the target) and I have tried uploading each of them individually,  in pairs and all three together and I always get the follwoing error:

Validation failed as:

  • One of your input PDBs -- native, alignment, or starting -- has a residue that is not found in the FASTA!


I am attaching one of the input PDBs (a small attachable one) which shows the above error even when uploaded individually, along with the target fasta and the dot bracket structure.

I have also tried by substituting all '(' or ')' to '.' in the dotbracket file for helical regions in the input PDB but that does not solve the error.

I will be thankful for any help.


Fri, 2021-10-08 00:29


We got the same error, for many cases which we tried to run using Stepwise program via browser. We tried with PDBs obtained from different modelling tools, having in mind, that there may be some problem with the PDB file, which we are not aware of. So we tried to upload 1zih and start_helix.pdb examples from Rosetta docs and it also shows the same error: 
One of your input PDBs -- native, alignment, or starting -- has a residue that is not found in the FASTA!

If someone could help with this issue, we would be very grateful.

Wed, 2024-03-20 02:11