From: João R. <an...@gm...> - 2012-04-17 18:18:55
|
Hello all, I'm using Pymol v1.5 (from fink, so open source version) to trace large scene that I have. To that end, I'm avoiding having PyMOL open and I wrote a small python script to do the rendering for me. All goes well, except this last part (don't mind the obvious variable names): cmd.ray(width, height, renderer=2) > <goog_409444192>cmd.png(default_name+'.png', dpi=300, ray=False) This actually renders my scene *twice. *I've tried cmd.do and it does the same.. am I missing something or is this not supposed to happen? Thanks and cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao |
From: Jason V. <jas...@sc...> - 2012-04-17 18:45:37
|
Hi João, What about cmd.png(default_name+'.png', dpi=300, ray=0) Cheers, -- Jason On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues <an...@gm...> wrote: > Hello all, > > I'm using Pymol v1.5 (from fink, so open source version) to trace large > scene that I have. To that end, I'm avoiding having PyMOL open and I wrote a > small python script to do the rendering for me. All goes well, except this > last part (don't mind the obvious variable names): > >> cmd.ray(width, height, renderer=2) >> cmd.png(default_name+'.png', dpi=300, ray=False) > > > This actually renders my scene twice. I've tried cmd.do and it does the > same.. am I missing something or is this not supposed to happen? > > Thanks and cheers, > > João [...] Rodrigues > http://nmr.chem.uu.nl/~joao > > > ------------------------------------------------------------------------------ > Better than sec? Nothing is better than sec when it comes to > monitoring Big Data applications. Try Boundary one-second > resolution app monitoring today. Free. > http://p.sf.net/sfu/Boundary-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: João R. <an...@gm...> - 2012-04-17 20:21:49
|
Same result Jason, i also tried =false... No dia 17 de Abr de 2012 20:45, "Jason Vertrees" < jas...@sc...> escreveu: > Hi João, > > What about > > cmd.png(default_name+'.png', dpi=300, ray=0) > > Cheers, > > -- Jason > > > On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues <an...@gm...> > wrote: > > Hello all, > > > > I'm using Pymol v1.5 (from fink, so open source version) to trace large > > scene that I have. To that end, I'm avoiding having PyMOL open and I > wrote a > > small python script to do the rendering for me. All goes well, except > this > > last part (don't mind the obvious variable names): > > > >> cmd.ray(width, height, renderer=2) > >> cmd.png(default_name+'.png', dpi=300, ray=False) > > > > > > This actually renders my scene twice. I've tried cmd.do and it does the > > same.. am I missing something or is this not supposed to happen? > > > > Thanks and cheers, > > > > João [...] Rodrigues > > http://nmr.chem.uu.nl/~joao > > > > > > > ------------------------------------------------------------------------------ > > Better than sec? Nothing is better than sec when it comes to > > monitoring Big Data applications. Try Boundary one-second > > resolution app monitoring today. Free. > > http://p.sf.net/sfu/Boundary-dev2dev > > _______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrödinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > |
From: Jason V. <jas...@sc...> - 2012-04-17 20:34:07
|
João, I'm not sure why this is giving you problems. Why do you have renderer=2? Why not the default? Are you counting primitives? If so, I suggest: cmd.set("ray_default_renderer", 2) # snapshot cmd.png(myFile, width=w, height=h, dpi=d, ray=0) # this will ray trace cmd.png(myFile, width=w, height=h, dpi=d, ray=1) Cheers, -- Jason On Tue, Apr 17, 2012 at 1:21 PM, João Rodrigues <an...@gm...> wrote: > Same result Jason, i also tried =false... > > No dia 17 de Abr de 2012 20:45, "Jason Vertrees" > <jas...@sc...> escreveu: > >> Hi João, >> >> What about >> >> cmd.png(default_name+'.png', dpi=300, ray=0) >> >> Cheers, >> >> -- Jason >> >> >> On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues <an...@gm...> >> wrote: >> > Hello all, >> > >> > I'm using Pymol v1.5 (from fink, so open source version) to trace large >> > scene that I have. To that end, I'm avoiding having PyMOL open and I >> > wrote a >> > small python script to do the rendering for me. All goes well, except >> > this >> > last part (don't mind the obvious variable names): >> > >> >> cmd.ray(width, height, renderer=2) >> >> cmd.png(default_name+'.png', dpi=300, ray=False) >> > >> > >> > This actually renders my scene twice. I've tried cmd.do and it does the >> > same.. am I missing something or is this not supposed to happen? >> > >> > Thanks and cheers, >> > >> > João [...] Rodrigues >> > http://nmr.chem.uu.nl/~joao >> > >> > >> > >> > ------------------------------------------------------------------------------ >> > Better than sec? Nothing is better than sec when it comes to >> > monitoring Big Data applications. Try Boundary one-second >> > resolution app monitoring today. Free. >> > http://p.sf.net/sfu/Boundary-dev2dev >> > _______________________________________________ >> > PyMOL-users mailing list (PyM...@li...) >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> > Archives: http://www.mail-archive.com/pym...@li... >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrödinger, LLC >> >> (e) Jas...@sc... >> (o) +1 (603) 374-7120 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: João R. <an...@gm...> - 2012-04-17 21:18:05
|
Hi Jason, I've tried a lot of stuff, thus the renderer=2.. (i installed povray and tried to use it). With the default option the result is the same. cmd.png(default_name+'.png', width, height, dpi, ray=0) Doing what you wrote still causes the renderer to kick in.. I'm a bit out of ideas.. Cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao No dia 17 de Abril de 2012 22:33, Jason Vertrees < jas...@sc...> escreveu: > João, > > I'm not sure why this is giving you problems. Why do you have > renderer=2? Why not the default? Are you counting primitives? If so, I > suggest: > > cmd.set("ray_default_renderer", 2) > > # snapshot > > cmd.png(myFile, width=w, height=h, dpi=d, ray=0) > > # this will ray trace > > cmd.png(myFile, width=w, height=h, dpi=d, ray=1) > > Cheers, > > -- Jason > > > On Tue, Apr 17, 2012 at 1:21 PM, João Rodrigues <an...@gm...> wrote: > > Same result Jason, i also tried =false... > > > > No dia 17 de Abr de 2012 20:45, "Jason Vertrees" > > <jas...@sc...> escreveu: > > > >> Hi João, > >> > >> What about > >> > >> cmd.png(default_name+'.png', dpi=300, ray=0) > >> > >> Cheers, > >> > >> -- Jason > >> > >> > >> On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues <an...@gm...> > >> wrote: > >> > Hello all, > >> > > >> > I'm using Pymol v1.5 (from fink, so open source version) to trace > large > >> > scene that I have. To that end, I'm avoiding having PyMOL open and I > >> > wrote a > >> > small python script to do the rendering for me. All goes well, except > >> > this > >> > last part (don't mind the obvious variable names): > >> > > >> >> cmd.ray(width, height, renderer=2) > >> >> cmd.png(default_name+'.png', dpi=300, ray=False) > >> > > >> > > >> > This actually renders my scene twice. I've tried cmd.do and it does > the > >> > same.. am I missing something or is this not supposed to happen? > >> > > >> > Thanks and cheers, > >> > > >> > João [...] Rodrigues > >> > http://nmr.chem.uu.nl/~joao > >> > > >> > > >> > > >> > > ------------------------------------------------------------------------------ > >> > Better than sec? Nothing is better than sec when it comes to > >> > monitoring Big Data applications. Try Boundary one-second > >> > resolution app monitoring today. Free. > >> > http://p.sf.net/sfu/Boundary-dev2dev > >> > _______________________________________________ > >> > PyMOL-users mailing list (PyM...@li...) > >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> > Archives: > http://www.mail-archive.com/pym...@li... > >> > >> > >> > >> -- > >> Jason Vertrees, PhD > >> PyMOL Product Manager > >> Schrödinger, LLC > >> > >> (e) Jas...@sc... > >> (o) +1 (603) 374-7120 > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrödinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > |
From: Pete M. <pa...@mc...> - 2012-04-17 23:00:16
|
It may be worth trying pymol 1.4 (instead of 1.5) - although this shouldn't make a difference, it might provide some more information (you also mentioned that you've got a large scene - depending on composition 1.4 may use less memory than 1.5). You may also want to try using a pml script vs python (start pymol with "-q -c your_raytrace_script.pml" arguments) and see if that helps, or at least breaks in different ways. Pete João Rodrigues wrote: > Hi Jason, > > I've tried a lot of stuff, thus the renderer=2.. (i installed povray and tried to use it). With the default option the result is the same. > > cmd.png(default_name+'.png', width, height, dpi, ray=0) > > Doing what you wrote still causes the renderer to kick in.. I'm a bit out of ideas.. > > Cheers, > > João [...] Rodrigues > http://nmr.chem.uu.nl/~joao > > > > No dia 17 de Abril de 2012 22:33, Jason Vertrees <jas...@sc...<mailto:jas...@sc...>> escreveu: > João, > > I'm not sure why this is giving you problems. Why do you have > renderer=2? Why not the default? Are you counting primitives? If so, I > suggest: > > cmd.set("ray_default_renderer", 2) > > # snapshot > > cmd.png(myFile, width=w, height=h, dpi=d, ray=0) > > # this will ray trace > > cmd.png(myFile, width=w, height=h, dpi=d, ray=1) > > Cheers, > > -- Jason > > > On Tue, Apr 17, 2012 at 1:21 PM, João Rodrigues <an...@gm...<mailto:an...@gm...>> wrote: >> Same result Jason, i also tried =false... >> >> No dia 17 de Abr de 2012 20:45, "Jason Vertrees" >> <jas...@sc...<mailto:jas...@sc...>> escreveu: >> >>> Hi João, >>> >>> What about >>> >>> cmd.png(default_name+'.png', dpi=300, ray=0) >>> >>> Cheers, >>> >>> -- Jason >>> >>> >>> On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues <an...@gm...<mailto:an...@gm...>> >>> wrote: >>>> Hello all, >>>> >>>> I'm using Pymol v1.5 (from fink, so open source version) to trace large >>>> scene that I have. To that end, I'm avoiding having PyMOL open and I >>>> wrote a >>>> small python script to do the rendering for me. All goes well, except >>>> this >>>> last part (don't mind the obvious variable names): >>>> >>>>> cmd.ray(width, height, renderer=2) >>>>> cmd.png(default_name+'.png', dpi=300, ray=False) >>>> >>>> This actually renders my scene twice. I've tried cmd.do and it does the >>>> same.. am I missing something or is this not supposed to happen? >>>> >>>> Thanks and cheers, >>>> >>>> João [...] Rodrigues >>>> http://nmr.chem.uu.nl/~joao >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Better than sec? Nothing is better than sec when it comes to >>>> monitoring Big Data applications. Try Boundary one-second >>>> resolution app monitoring today. Free. >>>> http://p.sf.net/sfu/Boundary-dev2dev >>>> _______________________________________________ >>>> PyMOL-users mailing list (PyM...@li...<mailto:PyM...@li...>) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>> >>> >>> -- >>> Jason Vertrees, PhD >>> PyMOL Product Manager >>> Schrödinger, LLC >>> >>> (e) Jas...@sc...<mailto:Jas...@sc...> >>> (o) +1 (603) 374-7120<tel:%2B1%20%28603%29%20374-7120> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrödinger, LLC > > (e) Jas...@sc...<mailto:Jas...@sc...> > (o) +1 (603) 374-7120<tel:%2B1%20%28603%29%20374-7120> > |
From: Thomas H. <sp...@us...> - 2012-04-18 07:38:13
|
Hi João, Pete & Jason, I think pml vs. py or 1.4 vs. 1.5 will make no difference. But I see two other things here: 1) renderer=2 is a "dry-run" according to the documentation, so it will not actually render a image. 2) if running in batch mode, there is no opengl window to capture from and PyMOL will always fall back to ray tracing, since it is the only way to obtain a figure in this mode. Cheers, Thomas Pete Meyer wrote, On 04/18/12 01:00: > It may be worth trying pymol 1.4 (instead of 1.5) - although this > shouldn't make a difference, it might provide some more information (you > also mentioned that you've got a large scene - depending on composition > 1.4 may use less memory than 1.5). > > You may also want to try using a pml script vs python (start pymol with > "-q -c your_raytrace_script.pml" arguments) and see if that helps, or at > least breaks in different ways. > > Pete > > João Rodrigues wrote: >> Hi Jason, >> >> I've tried a lot of stuff, thus the renderer=2.. (i installed povray and tried to use it). With the default option the result is the same. >> >> cmd.png(default_name+'.png', width, height, dpi, ray=0) >> >> Doing what you wrote still causes the renderer to kick in.. I'm a bit out of ideas.. >> >> Cheers, >> >> João [...] Rodrigues >> http://nmr.chem.uu.nl/~joao >> >> >> >> No dia 17 de Abril de 2012 22:33, Jason Vertrees <jas...@sc...<mailto:jas...@sc...>> escreveu: >> João, >> >> I'm not sure why this is giving you problems. Why do you have >> renderer=2? Why not the default? Are you counting primitives? If so, I >> suggest: >> >> cmd.set("ray_default_renderer", 2) >> >> # snapshot >> >> cmd.png(myFile, width=w, height=h, dpi=d, ray=0) >> >> # this will ray trace >> >> cmd.png(myFile, width=w, height=h, dpi=d, ray=1) >> >> Cheers, >> >> -- Jason >> >> >> On Tue, Apr 17, 2012 at 1:21 PM, João Rodrigues <an...@gm...<mailto:an...@gm...>> wrote: >>> Same result Jason, i also tried =false... >>> >>> No dia 17 de Abr de 2012 20:45, "Jason Vertrees" >>> <jas...@sc...<mailto:jas...@sc...>> escreveu: >>> >>>> Hi João, >>>> >>>> What about >>>> >>>> cmd.png(default_name+'.png', dpi=300, ray=0) >>>> >>>> Cheers, >>>> >>>> -- Jason >>>> >>>> >>>> On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues <an...@gm...<mailto:an...@gm...>> >>>> wrote: >>>>> Hello all, >>>>> >>>>> I'm using Pymol v1.5 (from fink, so open source version) to trace large >>>>> scene that I have. To that end, I'm avoiding having PyMOL open and I >>>>> wrote a >>>>> small python script to do the rendering for me. All goes well, except >>>>> this >>>>> last part (don't mind the obvious variable names): >>>>> >>>>>> cmd.ray(width, height, renderer=2) >>>>>> cmd.png(default_name+'.png', dpi=300, ray=False) >>>>> This actually renders my scene twice. I've tried cmd.do and it does the >>>>> same.. am I missing something or is this not supposed to happen? >>>>> >>>>> Thanks and cheers, >>>>> >>>>> João [...] Rodrigues >>>>> http://nmr.chem.uu.nl/~joao >>>> >>>> -- >>>> Jason Vertrees, PhD >>>> PyMOL Product Manager >>>> Schrödinger, LLC >>>> >>>> (e) Jas...@sc...<mailto:Jas...@sc...> >>>> (o) +1 (603) 374-7120<tel:%2B1%20%28603%29%20374-7120> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrödinger, LLC >> >> (e) Jas...@sc...<mailto:Jas...@sc...> >> (o) +1 (603) 374-7120<tel:%2B1%20%28603%29%20374-7120> -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: João R. <an...@gm...> - 2012-04-18 07:54:38
|
Thanks for the tips all of you. As I told Jason, the renderer option was the billionth thing I tried to make it work.. all default settings didn't. So it comes down to what Thomas said: if running in batch mode, there is no opengl window to capture from and > PyMOL will always fall back to ray tracing, since it is the only way to > obtain a figure in this mode. So, in a script, I shouldn't use ray. I should just use png directly and allow it to ray. It worked. Cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao No dia 18 de Abril de 2012 09:38, Thomas Holder < sp...@us...> escreveu: > Hi João, Pete & Jason, > > I think pml vs. py or 1.4 vs. 1.5 will make no difference. But I see two > other things here: > > 1) renderer=2 is a "dry-run" according to the documentation, so it will > not actually render a image. > > 2) if running in batch mode, there is no opengl window to capture from and > PyMOL will always fall back to ray tracing, since it is the only way to > obtain a figure in this mode. > > Cheers, > Thomas > > Pete Meyer wrote, On 04/18/12 01:00: > >> It may be worth trying pymol 1.4 (instead of 1.5) - although this >> shouldn't make a difference, it might provide some more information (you >> also mentioned that you've got a large scene - depending on composition 1.4 >> may use less memory than 1.5). >> >> You may also want to try using a pml script vs python (start pymol with >> "-q -c your_raytrace_script.pml" arguments) and see if that helps, or at >> least breaks in different ways. >> >> Pete >> >> João Rodrigues wrote: >> >>> Hi Jason, >>> >>> I've tried a lot of stuff, thus the renderer=2.. (i installed povray and >>> tried to use it). With the default option the result is the same. >>> >>> cmd.png(default_name+'.png', width, height, dpi, ray=0) >>> >>> Doing what you wrote still causes the renderer to kick in.. I'm a bit >>> out of ideas.. >>> >>> Cheers, >>> >>> João [...] Rodrigues >>> http://nmr.chem.uu.nl/~joao >>> >>> >>> >>> No dia 17 de Abril de 2012 22:33, Jason Vertrees < >>> jason.vertrees@schrodinger.**com <jas...@sc...> >>> <mailto:jason.vertrees@**schrodinger.com<jas...@sc...>>> >>> escreveu: >>> João, >>> >>> I'm not sure why this is giving you problems. Why do you have >>> renderer=2? Why not the default? Are you counting primitives? If so, I >>> suggest: >>> >>> cmd.set("ray_default_renderer"**, 2) >>> >>> # snapshot >>> >>> cmd.png(myFile, width=w, height=h, dpi=d, ray=0) >>> >>> # this will ray trace >>> >>> cmd.png(myFile, width=w, height=h, dpi=d, ray=1) >>> >>> Cheers, >>> >>> -- Jason >>> >>> >>> On Tue, Apr 17, 2012 at 1:21 PM, João Rodrigues <an...@gm... >>> <mailto:anar**yi...@gm... <an...@gm...>>> wrote: >>> >>>> Same result Jason, i also tried =false... >>>> >>>> No dia 17 de Abr de 2012 20:45, "Jason Vertrees" >>>> <jason.vertrees@schrodinger.**com <jas...@sc...> >>>> <mailto:jason.vertrees@**schrodinger.com<jas...@sc...>>> >>>> escreveu: >>>> >>>> Hi João, >>>>> >>>>> What about >>>>> >>>>> cmd.png(default_name+'.png', dpi=300, ray=0) >>>>> >>>>> Cheers, >>>>> >>>>> -- Jason >>>>> >>>>> >>>>> On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues <an...@gm... >>>>> <mailto:anar**yi...@gm... <an...@gm...>>> >>>>> wrote: >>>>> >>>>>> Hello all, >>>>>> >>>>>> I'm using Pymol v1.5 (from fink, so open source version) to trace >>>>>> large >>>>>> scene that I have. To that end, I'm avoiding having PyMOL open and I >>>>>> wrote a >>>>>> small python script to do the rendering for me. All goes well, except >>>>>> this >>>>>> last part (don't mind the obvious variable names): >>>>>> >>>>>> cmd.ray(width, height, renderer=2) >>>>>>> cmd.png(default_name+'.png', dpi=300, ray=False) >>>>>>> >>>>>> This actually renders my scene twice. I've tried cmd.do and it does >>>>>> the >>>>>> same.. am I missing something or is this not supposed to happen? >>>>>> >>>>>> Thanks and cheers, >>>>>> >>>>>> João [...] Rodrigues >>>>>> http://nmr.chem.uu.nl/~joao >>>>>> >>>>> >>>>> -- >>>>> Jason Vertrees, PhD >>>>> PyMOL Product Manager >>>>> Schrödinger, LLC >>>>> >>>>> (e) Jas...@sc...**<mailto:Jason.Vertrees@** >>>>> schrodinger.com <Jas...@sc...>> >>>>> (o) +1 (603) 374-7120<tel:%2B1%20%28603%29%20374-**7120> >>>>> >>>> >>> >>> -- >>> Jason Vertrees, PhD >>> PyMOL Product Manager >>> Schrödinger, LLC >>> >>> (e) Jas...@sc...**<mailto:Jason.Vertrees@** >>> schrodinger.com <Jas...@sc...>> >>> (o) +1 (603) 374-7120<tel:%2B1%20%28603%29%20374-**7120> >>> >> > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > |
From: Thomas H. <sp...@us...> - 2012-04-18 07:58:48
|
one more thing: PyMOL will not render twice if using prior=1: cmd.ray(..., renderer=0) cmd.png(..., prior=1) Cheers, Thomas João Rodrigues wrote, On 04/18/12 09:54: > Thanks for the tips all of you. As I told Jason, the renderer option was > the billionth thing I tried to make it work.. all default settings didn't. > > So it comes down to what Thomas said: > > if running in batch mode, there is no opengl window to capture from > and PyMOL will always fall back to ray tracing, since it is the only > way to obtain a figure in this mode. > > > So, in a script, I shouldn't use ray. I should just use png directly and > allow it to ray. It worked. > > Cheers, > > João [...] Rodrigues > http://nmr.chem.uu.nl/~joao -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |