[chimerax-users] building peptides in Chimera/ChimeraX

[Elaine Meng]

Hello Ishita,
Your question was forwarded.  I'm CC'ing chimerax-users at cgl.ucsf.edu (which is the recommended address for asking ChimeraX questions, for future reference).

Peptide-building in ChimeraX (and Chimera) does not predict the structure, it simply uses whatever angles you choose in the Build Structure tool.  So the reason it looks like a helix is that you told it to use the helix phi,psi angles.

ChimeraX build structure:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#start>

In the paper figure, it says that the indolicin structure is PDB 1g89 ... so if you want it to look like that, just open 1g89.  In the legend it says structures generated by Chimera, but apparently they just mean that images of the structures (from the PDB) were generated by Chimera.  1g89 is an NMR ensemble of 16 structures, so they apparently just chose one of the structures to show and hid the others.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> -------- Forwarded Message --------
> Subject:	Request regarding ChimeraX (From UC Davis)
> Date:	Wed, 17 Mar 2021 02:04:17 +0000
> From:	Ishita M Shah <imshah at ucdavis.edu>
> 
> Dear Dr. Ferrin, 
> I’m a Project Scientist at UC Davis and the newest user of ChimeraX. 
> I have a few questions regarding peptide secondary structure generation using ChimeraX. Would you please connect me to someone who could spare a few minutes to walk me through? 
> 
> Specifically, when I look up the secondary structure of Indolicidin (generated using Chimera) _ image attached from publication (it shows an extended structure), whereas, using Tools -> Structure editing -> Build Structure -> Start Structure -> Peptide/ Input sequence, the image I get is completely different (attached .bmp file). I really have basic requirements of prediction of secondary structures of peptides (and was using Indolicidin as an control) prior to exploring more. 
> 
> I apologize if this information regarding the use of ChimeraX for this purpose is readily available and that I could just be unaware of it. Any advice you can offer is highly appreciated.
> 
> Best,
> ishita. 
> 
> Ishita M. Shah, PhD
> Associate Project Scientist
> Associate Director, Microbial Programs
> Foods for Health Institute
> Department of Food Science and Technology
> University of California Davis
> 1221 Robert Mondavi Institute, South
> Davis, CA 95616
> Phone: (530) 754-7962
> 
> https://ffhi.ucdavis.edu/people/ishita-shah
> https://www.linkedin.com/in/ishita-m-shah-ph-d-a6a9664/
> 
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