Hi Maurice, Firstly, I would only recommend this type of work for generating a crude model, such as for a figure. I doubt that the quality would be high enough for work that depends on the detailed atomic coordinates. Energy minimization can only "rescue" local strains and conflicts, so if you start with something ridiculous you will still have something ridiculous after minimization! For a higher-quality model you would need to do more complicated conformational sampling and energy evaluation, either by creating it with some other program that includes such calculations, or by performing such calculations with another program after building the initial model in Chimera. Given those caveats, however, here are some ideas: (A) use Movement Mouse Mode (under Tools... Movement) set to "Move helix, strand, or turn" - this lets you move interactively whichever unit of secondary structure you "grab" with the mouse. You do not have to break any bonds, they will just distort. You can still move the entire structure when the cursor is in the window but not on top of any atoms. The drawback here is that instead of entering a specific angle you would have to approximate the amount of movement interactively. Before moving the helix, specify the center of rotation, for example by selecting one or more atoms and choosing Actions... Set Pivot or using the command cofr and specifying those atoms. The Movement Mouse Mode tool includes an "Undo Move" button so you can recover from mistakes. Save a PDB file of the result. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movemode/ movemode.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#actpivot http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb If you have a recent version of Chimera, you can measure the crossing angle of the original and modeled helices using the Axes tool (under Tools... Structure Analysis). http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#axes (B) if you really want to rotate the helix exactly X degrees, the only way I know of is to put that helix in a separate file. You could open the original file with the whole structure for comparison, and then a second file with just the helix. Move the structures in tandem to get a position where the rotation you want is around the screen axis X (horizontal in plane of screen), Y (vertical in plane of screen), or Z (normal to screen). Then freeze the original structure (for example by unchecking its Active box in the Model Panel, which is under Favorites), specify the center of rotation as in (A), and then use a command to rotate the helix: turn y 45 (or x or z depending on how you set up the view). Then save the PDB file of the helix "relative to" the original structure. To merge the helix back in, you would have to text-edit the whole structure file to replace the old coordinates with the new coordinates. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html After (A) or (B) and making sure you have saved those results to a file, you can consider whether or not minimization will improve the structure. I am skeptical that it would help very much. You would probably want to freeze some parts of the structure and do it in different stages freezing different sets of atoms to lessen distortions and keep the helix approximately in the intended orientation. I hope this helps, 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 On May 22, 2008, at 10:03 PM, Maurice Ho wrote:
Hi there, I would like to rotate a helix at a particular angle. How could I accomplish the following? 1. How to define the central axis of the helix in chimera? 2. How to set a particular angle to rotate? 3. I do this on a helix belonging to a GPCR, with the loops firstly broken for rotation and then perhaps need to rejoin them. How to join them back? 4. After joining, should I just redo energy minimization for the loops concerned? Much thanks!