Fei, The easiest way would be to use get_view/set_view. 1. Move your first frame pdb around until you're happy with the view 2. type get_view (pymol viewer window, or pymol gui window), and save the output in a new text file (I'd call it view.pml, but that's just me) 3. Load all of your frames in a script (which you're probably doing already), change "load frame2.pdb" to load frame2.pdb ; @view.pml" for all of your frames (or change whatever loop structure you're using).
This way all of your frames will be in the same scale, as well as orientation (which may not be what you're looking for). If you only want to control scale (not orientation), then you could probably work something up that only takes the scale parameters out of the orientation matrix. Hope this helps, Pete > Hi!: > I met a scaling problem. > I created many pdb files along one trajectory of DNA movement. I loaded each pdb file in pymol to create a picture, that is, one frame of the trajectory. Pymol shows each molecule in an optimal size automatically according the general shape of the molecular. The shape of the molecule along trajectory kept changing so that the size of the molecule also kept > changing. When I connected all the time frames together, I saw the funny effect that the molecule was jumping back and forth. > How can I put the molecule in the different time frames in exactly the same size? > Thanks! > Fei > > > > > > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > Pete Meyer Fu Lab BMCB grad student Cornell University
