From: Stephen J. B. <mup...@gm...> - 2011-10-27 17:36:35
|
I have a problem with lighting (I think) CGO lines, e.g., lineSet = [ > LINEWIDTH, 0.30, > BEGIN, LINES, > VECTOR, 0.0, 0.0, 0.0, > VECTOR, 1.0, 1.0, 1.0, > END, > ] > cmd.load_cgo( lineSet, 'LineSet' ) > For some reason, lines appear crisp from one angle, and strangely distorted from another angle (it's about 180deg for both -- think dark vs. light side of the moon: there is a crossover point). Here are links to two screen shots that show the problem: http://dl.dropbox.com/u/1209050/Screenshot-1.png http://dl.dropbox.com/u/1209050/Screenshot-2.png I have tried respositioning the lights (in the screenshot they're at the 6 faces of the box, marked by blue balls), but it doesn't change the viewing angle at all, only the shade of the lines. I have tried messing with the specular and spec_direct settings, but that only caused the lines to disappear completely (or rather, turn completely white). I also tried changing the ambiance settings, but that only changed the hue of the lines. I would really appreciate some help if anyone knows how to fix this. Thanks! Oh, and for reference, here's my system information: This Executable Build integrates and extends Open-Source PyMOL 1.3. > OpenGL graphics engine: > GL_VENDOR: NVIDIA Corporation > GL_RENDERER: GeForce 9500 GT/PCI/SSE2 > GL_VERSION: 3.2.0 NVIDIA 195.36.24 > Detected 8 CPU cores. Enabled multithreaded rendering. > I recently went pack to 1.3 as I was getting __very__ slow load times with 1.4. Cheers, Stephen --------------------------------- Stephen J. Bush sj...@un... PhD. Candidate | Bioinformatics & Computational Biology Tropsha Lab | UNC Chapel Hill |
From: Jason V. <jas...@sc...> - 2011-10-31 15:43:50
|
Hi Stephen, Does set two_sided_lighting, on help? Can you please send me a small script that reproduces the effect? I just tried your simple lineSet example (with fixes shown below) and everything worked fine: python from pymol.cgo import * from pymol import cmd lineSet = [ LINEWIDTH, 0.30, \ BEGIN, LINES, \ VERTEX, 0.0, 0.0, 0.0, \ VERTEX, 1.0, 1.0, 1.0, END, ] cmd.load_cgo( lineSet, 'lineSet' ) python end Cheers, -- Jason On Thu, Oct 27, 2011 at 1:36 PM, Stephen J. Bush <mup...@gm...> wrote: > I have a problem with lighting (I think) CGO lines, e.g., > >> lineSet = [ >> LINEWIDTH, 0.30, >> BEGIN, LINES, >> VECTOR, 0.0, 0.0, 0.0, >> VECTOR, 1.0, 1.0, 1.0, >> END, >> ] >> cmd.load_cgo( lineSet, 'LineSet' ) > > > For some reason, lines appear crisp from one angle, and strangely distorted > from another angle (it's about 180deg for both -- think dark vs. light side > of the moon: there is a crossover point). Here are links to two screen shots > that show the problem: > > http://dl.dropbox.com/u/1209050/Screenshot-1.png > http://dl.dropbox.com/u/1209050/Screenshot-2.png > > I have tried respositioning the lights (in the screenshot they're at the 6 > faces of the box, marked by blue balls), but it doesn't change the viewing > angle at all, only the shade of the lines. I have tried messing with the > specular and spec_direct settings, but that only caused the lines to > disappear completely (or rather, turn completely white). I also tried > changing the ambiance settings, but that only changed the hue of the lines. > > I would really appreciate some help if anyone knows how to fix this. Thanks! > > Oh, and for reference, here's my system information: > >> This Executable Build integrates and extends Open-Source PyMOL 1.3. >> OpenGL graphics engine: >> GL_VENDOR: NVIDIA Corporation >> GL_RENDERER: GeForce 9500 GT/PCI/SSE2 >> GL_VERSION: 3.2.0 NVIDIA 195.36.24 >> Detected 8 CPU cores. Enabled multithreaded rendering. > > > I recently went pack to 1.3 as I was getting __very__ slow load times with > 1.4. > > Cheers, > Stephen > > --------------------------------- > Stephen J. Bush > sj...@un... > > PhD. Candidate | Bioinformatics & Computational Biology > Tropsha Lab | UNC Chapel Hill > > ------------------------------------------------------------------------------ > The demand for IT networking professionals continues to grow, and the > demand for specialized networking skills is growing even more rapidly. > Take a complimentary Learning@Cisco Self-Assessment and learn > about Cisco certifications, training, and career opportunities. > http://p.sf.net/sfu/cisco-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 Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Stephen J. B. <mup...@gm...> - 2011-10-31 18:53:59
|
Hi Jason, Thanks for replying. Unfortunately, two sided lighting does not help. The example was just to show what I meant by CGO lines (I'm not sure how familiar everyone is with them). Here are links for 1) the *.py file that creates the objects shown in the images I previously provided and 2) the *.py file that places the new light objects (that still don't fix the problem). 1) http://dl.dropbox.com/u/1209050/3CMX_8_pock.py 2) http://dl.dropbox.com/u/1209050/lightDots.py Cheers, Stephen --------------------------------- Stephen J. Bush sj...@un... PhD. Candidate | Bioinformatics & Computational Biology Tropsha Lab | UNC Chapel Hill On Mon, Oct 31, 2011 at 11:43 AM, Jason Vertrees < jas...@sc...> wrote: > Hi Stephen, > > Does > > set two_sided_lighting, on > > help? > > Can you please send me a small script that reproduces the effect? > > I just tried your simple lineSet example (with fixes shown below) and > everything worked fine: > > python > from pymol.cgo import * > from pymol import cmd > lineSet = [ LINEWIDTH, 0.30, \ > BEGIN, LINES, \ > VERTEX, 0.0, 0.0, 0.0, \ > VERTEX, 1.0, 1.0, 1.0, END, ] > cmd.load_cgo( lineSet, 'lineSet' ) > python end > > Cheers, > > -- Jason > > On Thu, Oct 27, 2011 at 1:36 PM, Stephen J. Bush <mup...@gm...> > wrote: > > I have a problem with lighting (I think) CGO lines, e.g., > > > >> lineSet = [ > >> LINEWIDTH, 0.30, > >> BEGIN, LINES, > >> VECTOR, 0.0, 0.0, 0.0, > >> VECTOR, 1.0, 1.0, 1.0, > >> END, > >> ] > >> cmd.load_cgo( lineSet, 'LineSet' ) > > > > > > For some reason, lines appear crisp from one angle, and strangely > distorted > > from another angle (it's about 180deg for both -- think dark vs. light > side > > of the moon: there is a crossover point). Here are links to two screen > shots > > that show the problem: > > > > http://dl.dropbox.com/u/1209050/Screenshot-1.png > > http://dl.dropbox.com/u/1209050/Screenshot-2.png > > > > I have tried respositioning the lights (in the screenshot they're at the > 6 > > faces of the box, marked by blue balls), but it doesn't change the > viewing > > angle at all, only the shade of the lines. I have tried messing with the > > specular and spec_direct settings, but that only caused the lines to > > disappear completely (or rather, turn completely white). I also tried > > changing the ambiance settings, but that only changed the hue of the > lines. > > > > I would really appreciate some help if anyone knows how to fix this. > Thanks! > > > > Oh, and for reference, here's my system information: > > > >> This Executable Build integrates and extends Open-Source PyMOL 1.3. > >> OpenGL graphics engine: > >> GL_VENDOR: NVIDIA Corporation > >> GL_RENDERER: GeForce 9500 GT/PCI/SSE2 > >> GL_VERSION: 3.2.0 NVIDIA 195.36.24 > >> Detected 8 CPU cores. Enabled multithreaded rendering. > > > > > > I recently went pack to 1.3 as I was getting __very__ slow load times > with > > 1.4. > > > > Cheers, > > Stephen > > > > --------------------------------- > > Stephen J. Bush > > sj...@un... > > > > PhD. Candidate | Bioinformatics & Computational Biology > > Tropsha Lab | UNC Chapel Hill > > > > > ------------------------------------------------------------------------------ > > The demand for IT networking professionals continues to grow, and the > > demand for specialized networking skills is growing even more rapidly. > > Take a complimentary Learning@Cisco Self-Assessment and learn > > about Cisco certifications, training, and career opportunities. > > http://p.sf.net/sfu/cisco-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 > Schrodinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > |
From: Jason V. <jas...@sc...> - 2011-10-31 19:20:26
|
Hi Stephen, This looks like a bug. Please file it on the open-source bug tracker and we'll look into it. Cheers, -- Jason On Mon, Oct 31, 2011 at 2:53 PM, Stephen J. Bush <mup...@gm...> wrote: > Hi Jason, > > Thanks for replying. Unfortunately, two sided lighting does not help. The > example was just to show what I meant by CGO lines (I'm not sure how > familiar everyone is with them). > > Here are links for 1) the *.py file that creates the objects shown in the > images I previously provided and 2) the *.py file that places the new light > objects (that still don't fix the problem). > > 1) http://dl.dropbox.com/u/1209050/3CMX_8_pock.py > 2) http://dl.dropbox.com/u/1209050/lightDots.py > > Cheers, > Stephen > > --------------------------------- > Stephen J. Bush > sj...@un... > > PhD. Candidate | Bioinformatics & Computational Biology > Tropsha Lab | UNC Chapel Hill > > > On Mon, Oct 31, 2011 at 11:43 AM, Jason Vertrees > <jas...@sc...> wrote: >> >> Hi Stephen, >> >> Does >> >> set two_sided_lighting, on >> >> help? >> >> Can you please send me a small script that reproduces the effect? >> >> I just tried your simple lineSet example (with fixes shown below) and >> everything worked fine: >> >> python >> from pymol.cgo import * >> from pymol import cmd >> lineSet = [ LINEWIDTH, 0.30, \ >> BEGIN, LINES, \ >> VERTEX, 0.0, 0.0, 0.0, \ >> VERTEX, 1.0, 1.0, 1.0, END, ] >> cmd.load_cgo( lineSet, 'lineSet' ) >> python end >> >> Cheers, >> >> -- Jason >> >> On Thu, Oct 27, 2011 at 1:36 PM, Stephen J. Bush <mup...@gm...> >> wrote: >> > I have a problem with lighting (I think) CGO lines, e.g., >> > >> >> lineSet = [ >> >> LINEWIDTH, 0.30, >> >> BEGIN, LINES, >> >> VECTOR, 0.0, 0.0, 0.0, >> >> VECTOR, 1.0, 1.0, 1.0, >> >> END, >> >> ] >> >> cmd.load_cgo( lineSet, 'LineSet' ) >> > >> > >> > For some reason, lines appear crisp from one angle, and strangely >> > distorted >> > from another angle (it's about 180deg for both -- think dark vs. light >> > side >> > of the moon: there is a crossover point). Here are links to two screen >> > shots >> > that show the problem: >> > >> > http://dl.dropbox.com/u/1209050/Screenshot-1.png >> > http://dl.dropbox.com/u/1209050/Screenshot-2.png >> > >> > I have tried respositioning the lights (in the screenshot they're at the >> > 6 >> > faces of the box, marked by blue balls), but it doesn't change the >> > viewing >> > angle at all, only the shade of the lines. I have tried messing with the >> > specular and spec_direct settings, but that only caused the lines to >> > disappear completely (or rather, turn completely white). I also tried >> > changing the ambiance settings, but that only changed the hue of the >> > lines. >> > >> > I would really appreciate some help if anyone knows how to fix this. >> > Thanks! >> > >> > Oh, and for reference, here's my system information: >> > >> >> This Executable Build integrates and extends Open-Source PyMOL 1.3. >> >> OpenGL graphics engine: >> >> GL_VENDOR: NVIDIA Corporation >> >> GL_RENDERER: GeForce 9500 GT/PCI/SSE2 >> >> GL_VERSION: 3.2.0 NVIDIA 195.36.24 >> >> Detected 8 CPU cores. Enabled multithreaded rendering. >> > >> > >> > I recently went pack to 1.3 as I was getting __very__ slow load times >> > with >> > 1.4. >> > >> > Cheers, >> > Stephen >> > >> > --------------------------------- >> > Stephen J. Bush >> > sj...@un... >> > >> > PhD. Candidate | Bioinformatics & Computational Biology >> > Tropsha Lab | UNC Chapel Hill >> > >> > >> > ------------------------------------------------------------------------------ >> > The demand for IT networking professionals continues to grow, and the >> > demand for specialized networking skills is growing even more rapidly. >> > Take a complimentary Learning@Cisco Self-Assessment and learn >> > about Cisco certifications, training, and career opportunities. >> > http://p.sf.net/sfu/cisco-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 >> Schrodinger, LLC >> >> (e) Jas...@sc... >> (o) +1 (603) 374-7120 > > > ------------------------------------------------------------------------------ > Get your Android app more play: Bring it to the BlackBerry PlayBook > in minutes. BlackBerry App World™ now supports Android™ Apps > for the BlackBerry® PlayBook™. Discover just how easy and simple > it is! http://p.sf.net/sfu/android-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 Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |