need help joining existing pdb files with new sequence
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@ucdavis.edu
Hi John,
You can move an alpha helix or any part of structure by hand, for instance, select a helix by ctrl-click on one residue of its ribbon depiction, then press the up-arrow key. Then use menu Tools / Movement / Movevement Mouse Mode, choose “Move selection” in the dialog that appears, then you can rotate and translate with the mouse to move just the selected helix. Bonds from the helix to neighboring unselected residues will be messed up. If it is just one bond connecting the selected to unselected residues then you can avoid making that bond too long when you move the selected part by hand. Then you can improve the geometry near that bond by select the nearby residues and using energy minimization (menu Tools / Structure Editing / Minimize Structures) with the “fixed atoms” option set to “unselected”.
Tom
On Apr 28, 2016, at 12:09 PM, John Hess wrote:
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
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participants (2)
-
John Hess -
Tom Goddard