Hi :) Some people are just not lazy enough ;) Lazy people like me spend a good deal of effort thinking about how to avoid efforts like writing repetitive lines :p And then you could come up with:
from math import sin,pi mset 1 x300 for i in range(200,301): cmd.mdo( i, "set transparency,selection,%f" % ( math.sin( math.pi*(i-200)/(2*100) ) ) ) The fuzz with the sine is of course to have a smoother fade. One could also take the simpler linear fade, but mind that the either numerator or divisor (or both) have to be float in order to end up with a float: for i in range(200,301): cmd.mdo( i, "set transparency,selection,%f" % ( (i-200)/100.0 ) ) With a bit more scripting, you can easily use this to define functions for fading properties from one value to another over a given range of frames. As a side note, if the fade is part of a more complex movie, hide the surface one frame after the fade has completed. Possibly it's also best to explicitly show it again in the first frame, in case you have Pymol cycle through the movie. In case the purpose is fading in the surface, start with surface view hidden and turn on the surface the frame before you start the fade. This way you avoid Pymol calculating its way through a null surface, possibly even coming up with some artefacts... Hope it helps, Tsjerk On Tue, Sep 1, 2009 at 5:01 PM, Matthew D. Hogg<mh...@uvm.edu> wrote: > I use a clunky set of mdo commands to do this. > > mdo 266: set transparency, .1, (palm+linker+Nterm) > mdo 267: set transparency, .2, (palm+linker+Nterm) > mdo 268: set transparency, .3, (palm+linker+Nterm) > mdo 269: set transparency, .4, (palm+linker+Nterm) > mdo 270: set transparency, .5, (palm+linker+Nterm) > mdo 271: set transparency, .6, (palm+linker+Nterm) > mdo 272: set transparency, .7, (palm+linker+Nterm) > mdo 273: set transparency, .8, (palm+linker+Nterm) > mdo 274: set transparency, .9, (palm+linker+Nterm) > mdo 275: set transparency, 1, (palm+linker+Nterm) > > If the surfaces are turned on for objects palm, linker and Nterm, then > this will fade out the surface over frames 266 to 275. Setting the > transparency to 1 and then reversing the order of the values will make > the surface fade in. > > HTH > > Matthew Hogg > University of Vermont > Burlington, VT 05405 > > > Quoting Dirk Kostrewa <kostr...@genzentrum.lmu.de>: > >> Dear Warren, >> >> using PyMOL without any additional "plug-ins", like slerpy or eMovie, >> is it possible to fade in or out a surface of, say, a ligand, between >> scenes? >> >> Best regards, >> >> Dirk. >> >> ******************************************************* >> Dirk Kostrewa >> Gene Center, A 5.07 >> Ludwig-Maximilians-University >> Feodor-Lynen-Str. 25 >> 81377 Munich >> Germany >> Phone: +49-89-2180-76845 >> Fax: +49-89-2180-76999 >> E-mail: kostr...@genzentrum.lmu.de >> WWW: www.genzentrum.lmu.de >> ******************************************************* > > > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
