Re: [PyMOL] CGO rotate vs quaternion
Hi Pawel, Have a look here: http://euclideanspace.com/maths/algebra/realNormedAlgebra/quaternions/index.htm It should provide some insight into what quaternions are and how you can use them to rotate or obtain an axis-angle representation. Cheers, Tsjerk On Sun, Nov 24, 2013 at 11:31 PM, Павел Томашевский wrote: > Hi all, > > Ok, so today I have to admit that I don't know what quaternions are > but I will need to use them. > I'm working on PyMOL and Sensable Phantom Omni haptic device > integration using Virtual Reality Peripherial Network (VRPN). > > So far I have a nicely working plugin for PyMOL that can retreive > X,Y,Z coordinates and vector of four quaternion values. > > My CGO pointer (cone) can smoothly move according to X,Y and Z > changes. Now I need to do some rotations of the pointer. AFAIK > 'rotate' function accepts only degree value of rotation around axis. > > My question is: is there any build in PyMOL function that accepts four > quaternion values and do rotation (instead of degree for each axis)? > > If not: do you have any simple hint or math formulas for me :) to > calculate angles for rotation of CGO out of four quaternion value? > > Cheers > Pawel 'crooveck' Tomaszewski > > > -- > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up > now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > ___ > 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. -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk___ 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
Re: [PyMOL] ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282
Jason, My drivers are newest Nvidia 331.82 from http://www.nvidia.pl/download/driverResults.aspx/70559. I'm not sure if the problem is on my site or no. Maybe my pymol distribution is badly built? What else can I do to get rid of that bug? Cheers, Pawel 2013/11/24 Jason Vertrees : > Hi Pawel, > > I suggest making sure that your video drivers are up to date at all times > when using software like PyMOL. Mobile video cards notoriously badly > implement the OpenGL spec. > > If that's a bug in our part, we'll try to track it down. > > Cheers, > > -- Jason > > > On Sun, Nov 24, 2013 at 3:42 PM, Павел Томашевский > wrote: >> >> 2013/11/24 Jason Vertrees : >> > Hi, >> Hi Jason >> >> > Is there any chance you can send me your input file(s)? Also, please let >> > me >> > know what computer, video card, and architecture (32-bit/64-bit) you're >> > running on. >> >> So basically this problem occurs every time I start pymol, even >> without loading any input files. >> My computer is Dell Latitude E6400, running Windows 7 64-bits, I have >> Nvidia Quadro NVS160M. >> I've installed newest drivers a few days ago, but the problem still >> exists. >> >> If it matters... I've obtained PyMol executables (already compiled) >> from >> http://www.lfd.uci.edu/~gohlke/pythonlibs/3msnvi49/pymol-1.6.0.0.win-amd64-py2.7.exe. >> Executable comes with integrated Python 2.7 distribution... >> >> >> > Cheers, >> > >> > -- Jason >> >> Cheers >> Pawel >> >> >> > >> > >> > On Sat, Nov 23, 2013 at 2:47 PM, Павел Томашевский >> > wrote: >> >> >> >> Hello >> >> I run PyMol 1.6.0 on windows 7 and I get this error: >> >> ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns >> >> err=1282 >> >> or >> >> ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=1282 >> >> >> >> over and over again. >> >> Is there any way to get rid of that? That's really annoying. >> >> >> >> crooveck >> >> >> >> >> >> >> >> -- >> >> Shape the Mobile Experience: Free Subscription >> >> Software experts and developers: Be at the forefront of tech >> >> innovation. >> >> Intel(R) Software Adrenaline delivers strategic insight and >> >> game-changing >> >> conversations that shape the rapidly evolving mobile landscape. Sign up >> >> now. >> >> >> >> >> >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >> >> ___ >> >> 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 >> > >> > >> > >> > >> > -- >> > Jason Vertrees, PhD >> > Director of Core Modeling Products >> > Schrödinger, Inc. >> > >> > (e) jason.vertr...@schrodinger.com >> > (o) +1 (603) 374-7120 > > > > > -- > Jason Vertrees, PhD > Director of Core Modeling Products > Schrödinger, Inc. > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk ___ 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
Re: [PyMOL] ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282
Hi Pawel, I suggest making sure that your video drivers are up to date at all times when using software like PyMOL. Mobile video cards notoriously badly implement the OpenGL spec. If that's a bug in our part, we'll try to track it down. Cheers, -- Jason On Sun, Nov 24, 2013 at 3:42 PM, Павел Томашевский wrote: > 2013/11/24 Jason Vertrees : > > Hi, > Hi Jason > > > Is there any chance you can send me your input file(s)? Also, please let > me > > know what computer, video card, and architecture (32-bit/64-bit) you're > > running on. > > So basically this problem occurs every time I start pymol, even > without loading any input files. > My computer is Dell Latitude E6400, running Windows 7 64-bits, I have > Nvidia Quadro NVS160M. > I've installed newest drivers a few days ago, but the problem still exists. > > If it matters... I've obtained PyMol executables (already compiled) > from > http://www.lfd.uci.edu/~gohlke/pythonlibs/3msnvi49/pymol-1.6.0.0.win-amd64-py2.7.exe > . > Executable comes with integrated Python 2.7 distribution... > > > > Cheers, > > > > -- Jason > > Cheers > Pawel > > > > > > > > On Sat, Nov 23, 2013 at 2:47 PM, Павел Томашевский > > wrote: > >> > >> Hello > >> I run PyMol 1.6.0 on windows 7 and I get this error: > >> ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns > >> err=1282 > >> or > >> ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=1282 > >> > >> over and over again. > >> Is there any way to get rid of that? That's really annoying. > >> > >> crooveck > >> > >> > >> > -- > >> Shape the Mobile Experience: Free Subscription > >> Software experts and developers: Be at the forefront of tech innovation. > >> Intel(R) Software Adrenaline delivers strategic insight and > game-changing > >> conversations that shape the rapidly evolving mobile landscape. Sign up > >> now. > >> > >> > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > >> ___ > >> 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 > > > > > > > > > > -- > > Jason Vertrees, PhD > > Director of Core Modeling Products > > Schrödinger, Inc. > > > > (e) jason.vertr...@schrodinger.com > > (o) +1 (603) 374-7120 > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk___ 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
[PyMOL] CGO rotate vs quaternion
Hi all, Ok, so today I have to admit that I don't know what quaternions are but I will need to use them. I'm working on PyMOL and Sensable Phantom Omni haptic device integration using Virtual Reality Peripherial Network (VRPN). So far I have a nicely working plugin for PyMOL that can retreive X,Y,Z coordinates and vector of four quaternion values. My CGO pointer (cone) can smoothly move according to X,Y and Z changes. Now I need to do some rotations of the pointer. AFAIK 'rotate' function accepts only degree value of rotation around axis. My question is: is there any build in PyMOL function that accepts four quaternion values and do rotation (instead of degree for each axis)? If not: do you have any simple hint or math formulas for me :) to calculate angles for rotation of CGO out of four quaternion value? Cheers Pawel 'crooveck' Tomaszewski -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk ___ 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
Re: [PyMOL] ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282
2013/11/24 Jason Vertrees : > Hi, Hi Jason > Is there any chance you can send me your input file(s)? Also, please let me > know what computer, video card, and architecture (32-bit/64-bit) you're > running on. So basically this problem occurs every time I start pymol, even without loading any input files. My computer is Dell Latitude E6400, running Windows 7 64-bits, I have Nvidia Quadro NVS160M. I've installed newest drivers a few days ago, but the problem still exists. If it matters... I've obtained PyMol executables (already compiled) from http://www.lfd.uci.edu/~gohlke/pythonlibs/3msnvi49/pymol-1.6.0.0.win-amd64-py2.7.exe. Executable comes with integrated Python 2.7 distribution... > Cheers, > > -- Jason Cheers Pawel > > > On Sat, Nov 23, 2013 at 2:47 PM, Павел Томашевский > wrote: >> >> Hello >> I run PyMol 1.6.0 on windows 7 and I get this error: >> ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns >> err=1282 >> or >> ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=1282 >> >> over and over again. >> Is there any way to get rid of that? That's really annoying. >> >> crooveck >> >> >> -- >> Shape the Mobile Experience: Free Subscription >> Software experts and developers: Be at the forefront of tech innovation. >> Intel(R) Software Adrenaline delivers strategic insight and game-changing >> conversations that shape the rapidly evolving mobile landscape. Sign up >> now. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >> ___ >> 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 > > > > > -- > Jason Vertrees, PhD > Director of Core Modeling Products > Schrödinger, Inc. > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk ___ 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
Re: [PyMOL] ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282
Hi, Is there any chance you can send me your input file(s)? Also, please let me know what computer, video card, and architecture (32-bit/64-bit) you're running on. Cheers, -- Jason On Sat, Nov 23, 2013 at 2:47 PM, Павел Томашевский wrote: > Hello > I run PyMol 1.6.0 on windows 7 and I get this error: > ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282 > or > ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=1282 > > over and over again. > Is there any way to get rid of that? That's really annoying. > > crooveck > > > -- > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up > now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > ___ > 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 > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk___ 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
