[Chimera-users] building a alpha helix and flexing it

Anindito Sen emailanindito at yahoo.co.in
Fri Nov 21 15:48:45 PST 2008

Hi Elaine

Got the wrong email in extension in the previous email request. Please ignore it. Here is the problem- 

In continuation of the process (mentioned below) I have generated the
helix that needs to be added. However it seems that the helix needs to
be flexed in some points to get a better fit. Can yo let me know how do



Hi Andy,

There are two main possibilities:

(1) With the "addaa" command you can build out from the C-term of a  

protein, residue by residue.



(2) With the "Build Structure" tool you can create a peptide that is  

not attached to anything, then move it to a reasonable position and  

combine it with the existing protein.



The moving/combining part of #2 can be rather difficult, so if it is a  

C-terminal truncation, definitely #1 is the way to go.

For example, if the last residue in the structure is 309 in chain A of  

model #0, you could use commands like:

addaa ala,310,alpha #0:309.a

addaa lys,311,alpha #0:310.a

addaa thr,312,alpha #0:311.a

    ... etc. ...

If you need to extend the N-terminal end, however, approach #2 is the  

only choice.  In Build Structure (under Tools... Structure Editing),  

go to the "Add Atoms" tab and choose the "peptide sequence" option.   

There you would just enter the sequence in one-letter amino acid  

codes, specify alpha-helix backbone angles, indicate the new atoms  

should be put in a "new model" and click Add.  You don't want to put  

the helix in the same model as the protein because then you will not  

be able to move them separately.

Then get the helix into position by activating/deactivating models and  

using the mouse (deactivating a model freezes it so that only the  

other models move with the mouse).  Getting a reasonable position is  

nontrivial, unfortunately. Besides moving things interactively with  

the mouse, another possibility is to build enough atoms to overlap  

part of the protein structure and then match those overlapping parts,  

such as with the "match" command.

Once the helix is in a reasonable position relative to the protein,  

you could combine the models into one model and then add a bond.  If  

there were overlapping atoms, you would first need to delete the  

duplicate atoms.  Perhaps you only need a rough representation, and in  

that case do not need to combine and bond the structures.

See these previous posts for details on how to do the combining and  






I hope this helps,



Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu

UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab

Department of Pharmaceutical Chemistry

University of California, San Francisco


On Nov 18, 2008, at 12:55 PM, Anindito Sen wrote:

> Dear All

> I was wondering if there is any tool by which can generate an alpha  

> helix, as an extension of a truncated crystal structure docked in  

> the density map. The possibility of the truncated portion of the  

> protein behaving as an alpha helix has been predicted by different  

> groups. The density map shows some empty regions (after the crystal  

> structure has been docked) just good enough for an alpha helix to  

> fit in.

> Best

> Andy


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Chimera-users at cgl.ucsf.edu


Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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