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Remodel with residue constraints

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Remodel with residue constraints


I am trying to remodel a given structure where I want to replace a chain say B with same residues say alanines. How can I use remodel with constraints? To be more specific, how to write constraint files. I did look up the remodel documentation for the cst file. But, they describe atom level information. Is there a way to just do it at the residue level? (I mean, just give the residues I want to replace in the new structure?)

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Fri, 2017-03-10 01:40

I don't really understand your question.

If literally all you want to do is change the sequence - just use design (fixbb) instead.  This is the purpose of the resfile.

Most constraints in Rosetta are atomistic - this atom and this atom should be N angstroms apart.  If we want to constrain "residues" we generally constrain their CAs or CBs.  Constraints exist that function on whole residues but they're in less common use.  There are ways to use constraints to bias the designed sequence in certain ways - have 80% alanines or whatever - but I don't think that's what you're asking.

If you want to change the sequence AND use remodel for whatever purpose, and it is unclear how to do it with remodel alone - change the sequence first with fixbb and then use remodel afterward.

Fri, 2017-03-10 08:06

You should be able to specify residue identity during Remodel by using the Blueprint file. The syntax is similar to the one used in resfiles used by fixbb (and others). See for more details.

Mon, 2017-03-13 08:01