Ah Ha! Yes, that does the trick.... Many thanks to all for that solution!
-Tom -----Original Message----- From: Mauricio Esguerra [mailto:esgue...@rci.rutgers.edu] Sent: Monday, November 10, 2008 1:23 PM To: Thomas Stout Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] rotating "maps" ?? Hi Thomas, Try turn instead of rotate, that might work. Good luck, +++++++++++++++++++++++++++++++++++++++++++++++ + Mauricio Esguerra Neira + + T.A. and Graduate Student + + Wilma K. Olson Group + + Chemistry and Chemical Biology Department + + Rutgers, The State University of New Jersey + + Phone Number: 732-445-4619 + + Email: esgue...@eden.rutgers.edu + +++++++++++++++++++++++++++++++++++++++++++++++ On Mon, 10 Nov 2008, Thomas Stout wrote: > > Hi All -- > > I've just stumbled into an odd behavior that is either a bug, or more > likely my mis-understanding some aspect of how PyMOL works. I've > created "low resolution" surfaces on a hetero-meric protein complex to > illustrate the packing together of various protein chains. I've made > these surfaces somewhat transparent so that the underlying protein > chain can still be seen. > > Here's how the gaussian maps are made (a la Warren DeLano's recent > suggestions): > pymol> alter /proteinA, b=120 > pymol> alter /proteinB, b=120 > pymol> (etc) > pymol> alter /proteinA, q=1 > pymol> alter /proteinB, q=1 > pymol> (etc) > pymol> set gaussian_resolution, 4 > pymol> map_new mapA, gaussian, 1, /proteinA map_new mapB, gaussian, 1, > pymol> /proteinB > pymol> (etc) > > Now, for the odd behavior. After I've created figure one as above, I > want to rotate the complex by 90 degrees and create a figure viewing > down the orthogonal axis. If I click and drag with the mouse, all > objects rotate as expected. However, issuing: > pymol> rotate x, 90 > > results in the proteins rotating appropriately, but the gaussian maps > remain in place. Is there some setting required to allow > transformations to be applied to maps from the command line? > > Thanks, > Tom > > > > > This email (including any attachments) may contain material that is > confidential and privileged and is for the sole use of the intended > recipient. Any review, reliance or distribution by others or > forwarding without express permission is strictly prohibited. If you > are not the intended recipient, please contact the sender and delete > all copies. > > > Exelixis, Inc. reserves the right, to the extent and under > circumstances permitted by applicable law, to retain, monitor and > intercept e-mail messages to and from its systems. > This email (including any attachments) may contain material that is confidential and privileged and is for the sole use of the intended recipient. Any review, reliance or distribution by others or forwarding without express permission is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies. Exelixis, Inc. reserves the right, to the extent and under circumstances permitted by applicable law, to retain, monitor and intercept e-mail messages to and from its systems.
