[Chimera-users] Doubts regarding building a structure using Build Structure option

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 16 15:32:48 PDT 2014

Hi Ayush,
The main question is "why would you want to do this??!"

Build Structure is not meant for such a task, and there is no reason to regenerate a structure that you can already get from the Protein Databank.  In my opinion it would be extremely difficult, if not impossible, to do this.

To create exactly the same structure with building in Chimera, you would have to know ALL of the bond lengths, bond angles, and torsional angles of the original protein, and then set them painstakingly.  You would have to measure each of those things in the original structure.  Then in the copy, you couldn't just set the entire secondary structure phi/psi angles to the suggested values, either.  Instead you would have to enter exactly the phi and psi measured for each residue in the original structure for the corresponding residue in the new structure.   Even that would only be a tiny starting point, because you would still have to adjust all the sidechain torsion angles, and every single bond length and bond angle as well. 

Build Structure does allow creating peptides of defined sequence and changing torsion angles, bond lengths, and bond angles to exactly the values you specify.

Thus it should be possible in principle, but I think infeasible in practice, even if using commands where available (adjust, rotation).  So my best advice is "don't even try it!"
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 15, 2014, at 10:22 PM, "Garg, Ayush A." <garg.80 at buckeyemail.osu.edu> wrote:

> Dear Developer
> I was working with with UCSF Chimera. I was trying to reproduce structure 1V4S - Glucokinase structure using the Build Structure option under the tab Structure Editing in Tools. I have the sequence of the 455 amino acids and also know the sequence which is alpha helix, beta helix but the sequence of connectors between these structures is not a secondary structure. I was wondering how to reproduce those using your structure builder option. I have attached a word file with the sequence and the image of 1V4S in UCSF Chimera. I hope that will help you understand my doubt better. 
> Thank and Regards
> Ayush Arpit Garg
> Graduate Student 
> Ohio State University

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