Hi Zhong, When the first model is opened in Chimera and before it has been moved by the mouse or other means, its coordinate system is the same as Chimera's coordinate system (if you write out a PDB file at this point, the atom coordinates will be unchanged). Once the model is moved, its coordinates are transformed by the appropriate translation and rotation matrices to yield transformed coordinates. Saving a PDB file would then yield different coordinates than when the structure is first opened. Rotation parameters (e.g. xyz center of rotation) are in the same reference frame as these transformed coordinates. So, if the transformed coordinates of an atom were (3,4,5) and the center of rotation was (3,4,5) then the model would be rotating about that atom. I should mention that if you open a second model when another model is open, then the second model will be immediately transformed by the same rotations and translations that the first model is being transformed by. So if you have two structures that are supposed to be in certain relative positions according to their original coordinates, they will still be in those same relative positions when opened in Chimera, even if the first model is moved before the second model is opened. With many models open, a new model is transformed the same as the lowest-numbered model currently open. The meanings of the various rotation methods are described here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ sideview.html#rotation . There are also various commands/tools to help in moving models in specific ways. The Constrained Move tool (in the Movement category) allows you to use the mouse to translate/ rotate models on specified axes in the _model_ coordinate reference frame. The "reset" command moves models back to their positions when they were originally opened. The "turn" and "move" commands rotate and translate active models along/about specific axes in the Chimera reference frame. Hope this helps. Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Sep 7, 2005, at 4:01 PM, Huang, Zhong wrote:
Hi, dear chimera developers' I am a Chimera user of UT Medical school at Houston . Here I want to know how chimera rotates the loading structure. I wish to know what the rotation parameters mean? Which coordinate sysmtem they refere to? I check the on-line tutorial. Unfortunately, I didn't get the answer.
Best Zhong Huantg _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users