[Chimera-users] need help joining existing pdb files with new sequence

John Hess jfhess at ucdavis.edu
Thu Apr 28 12:09:50 PDT 2016


HI folks,

I have asked Elaine a couple questions about this project of mine. She’s been very helpful, but I’m such a beginner, I feel guilty wasting her time and the rest of the folks reading the entire chimera list as I ask how to connect this and move that.

I would like to take at least 2 existing pdb files and link them to some additional peptides sequence that would be between them.  The resulting pdb would describe a structure that looks like this:

> protein 1 -> peptide linker -> protein 2

I’m dealing mainly with alpha helices (in coiled-coils), and I know how I want them positioned.  I joined a helical peptide sequence (made using Build Structure) to one pdb file but the orientation was way off and I’m wondering how to “grab” the entire helical peptide region and move it where I want it (sorry, in the past, I have tried to modify structures with Foldit and have had a collaborator who used Rosetta to try and model my data.).

Is anyone else on this list from UC Davis and willing to get together for some tutoring?  Does anyone not at Davis have time to answer my questions and help?  If we work well by email and I make progress, I think that this could be a $ for time or co-authorship situation.

thanks,

John Hess
jfhess at ucdavis.edu






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