On Feb 12, 2008, at 9:35 PM, Aguang Dai wrote:
I'm a Chimera user in FSU. I would like to use Chimera to build some models. I used 'turn' command to rotate the model around the z axis. The command and option was: turn z 27.6923. The model is from a PDB file. But the result was that it should have be, not what I wanted. The atoms should be always in the circle centered in the Z axis, respectively.
So my question is: When Chimera open a PDB file recording a protein structure, whether the coordinate axis is exactly the same as that in the PDB file? Thank you for your information in advance. Best, Daniel
Hi Daniel, As Tom mentioned, rotation axes are defined relative to the viewer, as described here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html and for the input coordinates to match those axes, they must be untransformed (not moved after opening, or "reset" to the initial position). Even after resetting, I am not sure whether the center of rotation will be where you want it, however, so here are some additional suggestions: (A) you can change the center of rotation. See the Rotation tool (under Tools... Movement) for how the center is calculated and how to change it: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#rotation (B) you can use a rotation axis defined by the molecule coordinates instead of the view, even if you have rotated that molecule (Tools... Movement... Constrained Move). Disadvantages of this tool are that it only applies to interactive mouse movement (not with commands like "turn"), and when it is turned on, you can only rotate about that one axis, so usually one keep turning it on and off to get the position you want. I hope this helps. If you are still having trouble after trying Tom's or my suggestions, please also send the PDB file you are using - that would help us understand what you are trying to do. You could just send it to me if you don't want to send to the whole list. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html