[Chimera-users] Peptide Builder in 1.4x

James Nettles jnettle at emory.edu
Wed Feb 10 14:11:46 PST 2010

That was it. I couldn't tell that I needed to explicitly set the  
angles for this version. Makes sense now.

Thanks for the quick response.


On Feb 10, 2010, at 4:50 PM, Elaine Meng wrote:

> 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  
> arbitrarily.
> 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
> -----
> 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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