[Chimera-users] Adjust angle

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 19 10:26:19 PDT 2011

Hello Thomas!
Chimera is intended for a broad range of uses, visualization/analysis of small molecules to macromolecules to assemblies, and it has some atomic-level building capabilities.   There is just more "competition" in the world of molecular modeling programs for those more traditional uses.

Currently you can change bond lengths and torsion angles (dihedrals, defined by 4 atoms), but there is nothing specifically for bond angles (defined by 3 atoms). I say "specifically" because you could select the atoms on one side and use "movement mouse mode"  (under Tools... Movement) to manually position them with the mouse.  However, it is probably difficult to do that without changing the bond length or moving A3 out of the original A1-A2-A3 plane.  Perhaps if you used the commands "align" and "turn" first to put A1-A2-A3 exactly in the plane of the screen, set pivot at A2, and then use the mouse near the edge of the window (outside the trackball) to perform a pure Z-rotation.

The Build Structure tool (under Tools... Structure Editing) has tabs for creating a new structure, building outward from existing structures, modifying atom types, changing bond lengths, joining fragments together.  If you Ctrl-doubleclick a bond, there will be a context menu including the choice to "rotate bond", meaning to modify the dihedral angle with the Adjust Torsions tool.  There are also some commands that modify structures (addaa, swapaa, swapna, bond, ...)


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 Apr 19, 2011, at 9:55 AM, Thomas Mitterfellner wrote:

> Hello!
> My question is: it possible not just to measure but to change the angle 
> between three atoms (e.g. A1 and A2 fixed, A3 rotated in the plane 
> spanned by A1-A2-A3 with radius A2-A3)?
> What I really like in Chimera (and miss in other molecular modelling 
> software) is the possibility to move/rotate only the atoms selected, 
> which is great e.g. for pre-aligning two molecular fragments when 
> modelling transition states.
> I know chimera is actually rather intended to be used for large 
> molecules but it could be a great tool for modifying/building structures 
> if only it was easier to modify structural parameters like bond lengths, 
> angles and torsions (which I saw is possible).
> Kind regards,
> Thomas Mitterfellner

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