[Chimera-users] building a alpha helix and flexing it
emailanindito at yahoo.co.in
Fri Nov 21 15:48:45 PST 2008
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
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.
Chimera-users mailing list
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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