Error in Protein-DNA design using rosettascripts #377
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Hi! In the protein_DNA design process, I met this problem: ERROR:: Exit from: src/protocols/dna/RestrictDesignToProteinDNAInterface.cc line: 269 File: src/protocols/dna/RestrictDesignToProteinDNAInterface.cc:269 protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol: File: src/protocols/dna/RestrictDesignToProteinDNAInterface.cc:269 Would anyone please tell me what does "top strand" mean? I write the TaskOperations like this: "RestrictDesignToProteinDNAInterface name="designchainc" dna_defs="C.109.THY" base_only="1" z_cutoff="3.0"" I ran successful without the "designchaind" taskoperation but I still want to operate the chain D since those two bases are the ones interact with the protein. If I change the "D.224.CYT,D.225.THY" to their complementary bases on chain C , will it be the same ? Or there is other solutions to solve this problem? Thank you for your help. |
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Digging through the code, it's a little confusingly written, but it does look like the issue is that when setting So I believe you are correct in that you should be able to change things from the D chain to the complementary based on chain C, and get things to work. (From what I can tell, there's no difference in treatment between the top and bottom residue in the base pair -- if you specify one, they're both treated. But that does raise the question about why it's particular about only specifying the top base. Best I can tell it's merely a programming consideration due to the way the data is stored internally.) |
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Thank you for your help! |
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Digging through the code, it's a little confusingly written, but it does look like the issue is that when setting
dna_defs, RestrictDesignToProteinDNAInterface expect the indicated residues to be the "top" residue of the base pair. From what I can tell, the "top" residue is simply the residue which comes first in the structure.So I believe you are correct in that you should be able to change things from the D chain to the complementary based on chain C, and get things to work.
(From what I can tell, there's no difference in treatment between the top and bottom residue in the base pair -- if you specify one, they're both treated. But that does raise the question about why it's particular …