Hi, I'm currently working on a gp140 model and have docked coordinates for 2 different conformations. I am trying to measure the rotation between the docked coordinates using the method in the EM-fit tutorial and i had a few questions. How does the "measure rotation #1 #3 showslab true" command measure the rotation? How does it determine the axis of rotation? Is it possible for me to create my own axis? Is there any way to increase the size of the slabs (they are too small visually)? -Thanks!
Hi Jeffrey, The "measure rotation" command determines the rotation between the coordinate frames of two models that have been moved relative to one another. A rigid motion involves a rotation and a translation. The rotation axis direction and angle is uniquely determined (for rotation angles > 0) but the axis could go through any point in space. Using axes that go through different points just changes the translation needed to achieve the rigid motion. There is a point you can choose the rotation axis to go through such that the translation needed is only parallel the rotation axis. Basically the rigid motion consists of a rotation about this axis, and a translation parallel to that axis. That is the rotation axis placement given by "measure rotation". It does not allow you to place the axis wherever you want. There is currently no option in the measure rotation command to make the slab display larger. You can edit a Python file chimera/share/MatchDomains/__init__.py changing the lines near the end e = 2 # Factor for enlarging square dz = chimera.cross(axis, sq1) * .05 # Thickness vector to say e = 4 dz = chimera.cross(axis, sq1) * .1 to make the slabs bigger. I'll add a feature request to improve the measure rotation command to include slab size options. Tom
Hi, I'm currently working on a gp140 model and have docked coordinates for 2 different conformations. I am trying to measure the rotation between the docked coordinates using the method in the EM-fit tutorial and i had a few questions. How does the "measure rotation #1 #3 showslab true" command measure the rotation? How does it determine the axis of rotation? Is it possible for me to create my own axis? Is there any way to increase the size of the slabs (they are too small visually)?
-Thanks!
Hi Jeffrey, As an alternative: Chimera also allows defining planes and axes from whatever sets of atoms you like, and making measurements that involve these objects. I don't know how well it applies to your situation, but you could define two planes from corresponding sets of atoms in the two structures, then get the angle between those planes. This can be done with the "Axes/Planes/Centroids" tool (under Tools.... Structure Analysis), or in scripts with the commands "define" and "angle". <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 4, 2011, at 6:58 PM, Jeffrey Hu wrote:
Hi, I'm currently working on a gp140 model and have docked coordinates for 2 different conformations. I am trying to measure the rotation between the docked coordinates using the method in the EM-fit tutorial and i had a few questions. How does the "measure rotation #1 #3 showslab true" command measure the rotation? How does it determine the axis of rotation? Is it possible for me to create my own axis? Is there any way to increase the size of the slabs (they are too small visually)?
-Thanks!
participants (3)
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Elaine Meng -
Jeffrey Hu -
Tom Goddard