[Chimera-users] Peptide Builder in 1.4x

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 10 13:50:12 PST 2010

Hi Jim,
I just tried this and it is working fine for me in the 1.4 release.   
Here are the steps that I tried:

(1) start Build Structure
(2) in Add Atoms tab, choose "peptide sequence" and enter sequence  
AAAAKVLKDD (for example)
(3) click Add, which raises secondary dialog for setting backbone angles
(4) the secondary dialog initially has all angles set for alpha-helix;  
you can choose a different secondary structure, e.g. "antiparallel  
beta strand" (but this won't have an effect until the following steps)
(5) choose the rows to which you want to apply those angles using the  
mouse; I used click-drag to choose all the rows
(6) click the "Set" button right below the list of residues to fill in  
those rows with the desired angles.  I just noticed this button is  
blank in the mac aqua version... maybe that led to confusion?   
Clicking it still works, though.  It should look like

[Set] selected rows to phi[phi-value] psi[psi-value]

where the [Set] part is a button.

(7) click Apply or OK (which also dismisses the dialog) to create the  
peptide with the phi/psi angles that are listed in the table

Step 4 is for your convenience if you know what secondary structure  
you want.  You can also edit the angle values in the "Set" line  

Let us know if this series of steps is not working for you.  You can  
use "Help... Report a Bug" in the Chimera menu to report bugs, which  
would automatically include information about exactly which build you  
are using and what kind of computer you are using.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 10, 2010, at 1:26 PM, nettles wrote:

> Hi All,
> I was very excited to download the 1.4 version of Chimera with it  
> many improved features yesterday.
> However, I was surprised today when I tried to build an anti  
> parallel beta sheet and it came out looking like an alpha helix.  
> After experimenting around i realized all option give alpha helix.  
> This is true for 1.4 (build 26788) and 1.4.1 (build 29977)and . The  
> old version 1 build 2540 works fine. (It worked with a newer version  
> I had too, but silly me overwrote that with the 1.4.x)
> Thought you would like to know.
> I appreciate your excellent software.
> Thanks,
> Jim Nettles_______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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