[Chimera-users] building a peptide

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 30 09:34:30 PDT 2013


Hi Kumud,
You would just specify the phi and psi angles for "turn" when building the peptide.  You can specify a different phi and psi for each residue if you want, in the peptide building dialog.  You do not have to use the values supplied for alpha and beta, you can enter any values, as described in the instructions:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>

 Also, in a peptide structure that already exists, you can change phi and psi for each residue, either

...by rotating the bond interactively (see the Adjust Torsions tab in Build Structure):
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust>
or
...by changing the "phi" and "psi" attribute values in the Selection Inspector (select an amino acid residue in a peptide or protein, click green  magnifying glass near bottom right of Chimera window to open the Inspector, Inspect: "Residue" and change the values for "phi angle" and "psi angle")  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>

However, it is up to you to specify reasonable values.  You can check the Ramachandran map by using the "Ramachandran plot" function in the Model Panel (under Favorites in the menu).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/ramachandran.html>

Although it is possible to build a whole protein with different secondary structures, it would probably have many severe problems (packing etc.) and the basic peptide-building in Chimera is *not* intended for this purpose.  You might want to look into using some other program to predict structure instead, or modify an existing protein structure instead of building the whole thing from scratch.  There are probably hundreds of programs and dozens of web servers to predict protein structure, but it is beyond the scope of the chimera-users list and my knowledge to discuss the possibilities.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 29, 2013, at 11:50 PM, Kumud Agarwal wrote:

> Hi,
> Thank you for your help.
> Is there any way to build a beta sheet in Chimera? How can I introduce
> turns in between the strands in beta sheet using the build structure
> option in chimera?




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