[Chimera-users] Peptide Builder in 1.4x

[Eric Pettersen]

In tomorrow's daily build, the 'Set' button will show it's text in the  
mac aqua version.

--Eric

On Feb 10, 2010, at 2:11 PM, James Nettles wrote:

>
>
> 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.
>
> Jim
>
> 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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