[Chimera-users] "docking" animation

Tom Goddard goddard at cgl.ucsf.edu
Fri Dec 5 09:20:06 PST 2008

Hi Andy,

  Elaine's earlier mailing list messages describe how to create the new 
alpha helix.   If you have the alpha helix as part of the atomic model 
and need to move it and distort it to fit the map, here are suggestions.

  There are only two Chimera tools I can think of that are going to be 
of much use for this.  The first is Movement Mouse Mode (menu Tools / 
Movement).  It allows you to select any set of atoms and move them 
however you want with the mouse while the other parts of the model are 
frozen in place.  That is going to produce bad bond geometry and the 
Minimize Structure tool (Tools / Structure Editing) may be able to fix 
those if the distortions are not too great.  I don't have any experience 
trying that on hand-moved alpha-helices so don't know how likely it is 
to work.  The Movement Mouse Mode tool will require moving a number of 
different subsegments of the alpha helix to introduce a bend.  There are 
no specialized tools in Chimera that would bend an alpha helix in a 
continuous way.  In general Chimera capabilities to fit flexible atomic 
models in maps are extremely primitive.


Anindito Sen wrote:
> Hi Elaine
> 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 that?
> Thanks
> Andy

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