From: Buz B. <bu...@ma...> - 2008-12-15 19:41:53
|
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 |
From: Nathaniel E. <nat...@gm...> - 2008-12-15 22:23:50
|
On Mon, Dec 15, 2008 at 11:41 AM, Buz Barstow <bu...@ma...> wrote: > 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? > Translate every model so that the center is at the origin, then use the set_view command to apply the same viewing matrix for each model. (You can still rotate the models, just don't zoom.) I'm not sure if there's already a simple way to do the translation from within PyMOL, but it should be quite straightforward using cctbx or CNS or something similar. -Nat |
From: DeLano S. <de...@de...> - 2008-12-16 21:06:17
|
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:su...@de... > -----Original Message----- > From: Buz Barstow [mailto:bu...@ma...] > Sent: Monday, December 15, 2008 11:42 AM > To: pym...@li... > 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 > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Buz B. <bu...@ma...> - 2008-12-18 23:26:54
|
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:su...@de... > > > >> -----Original Message----- >> From: Buz Barstow [mailto:bu...@ma...] >> Sent: Monday, December 15, 2008 11:42 AM >> To: pym...@li... >> 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 >> PyM...@li... >> 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.com/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |