[Chimera-users] Peptide Builder in 1.4x
pett at cgl.ucsf.edu
Wed Feb 10 14:16:27 PST 2010
In tomorrow's daily build, the 'Set' button will show it's text in the
mac aqua version.
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.
> 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
>> (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.
>>> Jim Nettles_______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
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