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I'm using antibody protocl to graft some models but it fails with the following error:
ERROR: Unxpected length of light-fr3 [length=31], length expected to be: [32, 33, 34]!
Do you have any comments on this? I have three sequences (three different antibodies with light and heavy chains) and it works on one of them but the same error on the two others.
Thanks a lot in advance,
I would like to generate fragments for protein sequence structure prediction ab initio locally, on my laptop, without involving any server, such as Robetta. I carry out it with a help of make_fragments.pl script. And I met with several problems with make_fragment.pl dependencies. I want to solve these problems. Could you advise me, if you can, how to solve them, please?
My first problem consists in follows:
in ddg_monomer module, we have encountered a problem with the length of the PDB file name when predicting mutant with 50+ mutations. Since Rosetta constructs the PDB file name based on the mutations included in the predicted mutant as prefix + list of mutations, with a large number of mutations this file name can be longer than 255 characters which causes the file system to be unable to store the PDB file. Is there any way how to prevent this behavior, for example set rosetta to store PDB file under user given name? Thank you for you answer.
I'm a postgraduate student, interested in protein structure prediction.
I noticed that the document said:
- Abinitio: max 150 amino acids are cosidered possible
So, I want to know, how to use rosetta to predict number of protein of amino acids more than 150 (e.g. 500)?
i have suplied Farafar2 with an RNA sequences of length 47. the server returns a complete circular structure. i dont have a template and am just giving the fasta file. when i give the dot-bracket structure along with the fasta file, it returns an error too.
I am trying to build a model for my protein and I have a medium resolution map (~5-6 A). I tried backbone tracing manually, but many regions are dubious. This protein does not have any homologous protein either, so I am looking for tools to do denovo model building with guided electron density. Is there any available protocol to achieve this?