> 1. Use the grid_mode option (only available in the compiled from > source pymols)
FYI: grid_mode and many other enhancements will be present in the soon-to-be-available PyMOL 1.2 BETA builds. The annual PyMOL release cycle for "official" PyMOL builds has settled down as follows: - Summer: The major annual release is cut in June/July, followed by any necessary patch/updates during the summer so that we enter the academic cycle with a robust build intended for widespread adoption. - Fall: We hunker down and tackle the toughest development challenges for the year, issuing few releases since the code at its most unstable and incompatible condition. - Winter: Starting in January, we begin issuing a series of routine beta builds with all the new stuff, so that the bold and the daring can try things out and begin reporting any issues. - Spring: We freeze the feature set then stabilize and test everything as much as possible in anticipation of the robust major release at the start of summer. Of course, the open-source "trunk" is available to developers at any time of the year :). Cheers, Warren > -----Original Message----- > From: Buz Barstow [mailto:b...@mac.com] > Sent: Thursday, December 18, 2008 3:27 PM > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Ray Tracing A Protein Gallery > > Dear All, > > Thanks for all your suggestions on ray tracing the protein gallery. > > In the end, I used several of the techniques suggested, and everything > worked out really well! > > To summarize: > > 1. Use the grid_mode option (only available in the compiled from > source pymols) > 2. Make a fake .pdb that has the corners and centers of a 3D box to > use for alignment > 3. Use the set_view command to apply the same viewing matrix > 4. Use the zoom command with a center and a distance specified. > > Also, the cealign package is really helpful for aligning and > translating very dissimilar molecules. > > Thanks! and all the best, > > --Buz > > > > > On Dec 16, 2008, at 4:05 PM, DeLano Scientific wrote: > > > Hi Buz, > > > > You can use "center" as a selection name for input with zoom, along > > with a > > distance value. > > > > zoom center, distance > > > > e.g. > > > > # first, get the object you want in the center of the screen > > > > orient > > > > # then zoom the viewer by a fixed amount about the center point > > > > zoom center, 10 > > > > # you may also wish to move the clipping planes in/out to avoid > > cutting into > > any of the molecular representations: > > > > clip atoms, 4, selection=all > > > > # also, depending upon the application, you might want to disable > > perspective > > > > set orthoscopic > > > > # get rid of background pixels > > > > unset opaque_background > > > > # render > > > > ray > > > > # and save > > > > save struct001.png > > > > Cheers, > > Warren > > > > > > -- > > DeLano Scientific LLC > > Subscriber Support Services > > mailto:supp...@delsci.com > > > > > > > >> -----Original Message----- > >> From: Buz Barstow [mailto:b...@mac.com] > >> Sent: Monday, December 15, 2008 11:42 AM > >> To: pymol-users@lists.sourceforge.net > >> Subject: [PyMOL] Ray Tracing A Protein Gallery > >> > >> Dear All, > >> > >> I'm making a gallery of protein molecules for my PhD thesis. > >> I'd like to find an automatic way to ensure that all of the > >> ray traced images have the same scale. Is there an easy way > >> to do this? > >> > >> Thanks! and all the best, > >> > >> --Buz > >> > >> -------------------------------------------------------------- > >> ---------------- > >> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las > >> Vegas, Nevada. > >> The future of the web can't happen without you. Join us at > >> MIX09 to help pave the way to the Next Web now. Learn more > >> and register at > >> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009 > > .visitmix.com/ > >> _______________________________________________ > >> PyMOL-users mailing list > >> PyMOL-users@lists.sourceforge.net > >> https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > ------------------------------------------------------------------------ > ------ > > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, > > Nevada. > > The future of the web can't happen without you. Join us at MIX09 to > > help > > pave the way to the Next Web now. Learn more and register at > > > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix. co > m/ > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > ------------------------------------------------------------------------ -- > ---- > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, > Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix. co > m/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > >
