Re: [PyMOL] New plugin and Doubt with APBS Tools
We discussed this a bit off-list, and it looks like this was the answer: The potentials are assigned to points in space. That's why the isosurfaces don't change, and also why the surface coloring changes when you change the shape of the surface. Hope that helps anyone else who might have this question, -michael On 1/9/07, Michael Lerner wrote: Raúl, I don't have time to look at this in detail right now, but .. what exactly do you mean that the potentials change between frames? What happens if you draw isosurfaces? Do they change? -michael On 1/7/07, Raúl Mera wrote: > Dear all, > > Two things. > First, I just written a small plugin that uses the > program "reduce" to add hydrogens to a molecule or to > a trajectory loaded in Pymol.(since each frame of the > trajectory is hydrogenated by reduce, I think that > protonation states could vary between frames) This > allow us to have a reliable protonation method in > PyMOL, without having to save the structure as PDB and > hydrogenate with another app, and using an open-source > (as far as I know) and easy to install application. > > Since I don't have any website right now, I will try > to make it available from the Pymol Wiki. If you want > the plugin right now, just e-mail me. > > The other thing is a doubt in using the APBS Tools. > When I use it to calculate electrostatics potentialsof > a trajectory (but the PQR is made by PDB2PQR from a > PDB made with PyMOL, i.e, only from the first > snapshot) > I get a .dx map that I think has the potentials only > for the first frame. When I display the potential > surface in the trajectory, the potentials seems to > change between frames, which I wouldn't expect since I > think that the calculation was performed only for the > first frame. > My doubt is: Are these changes alleatory due to a > change > of the structure's position changes on the grid, or > they have some significance?, if the latter, what > significance? (maybe the changes are produced by the > motion of polar groups?) > > Thanks in advance, > > Raul > > __ > Correo Yahoo! > Espacio para todos tus mensajes, antivirus y antispam ¡gratis! > Regístrate ya - http://correo.espanol.yahoo.com/ > > - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net
Re: [PyMOL] New plugin and Doubt with APBS Tools
Raúl, I don't have time to look at this in detail right now, but .. what exactly do you mean that the potentials change between frames? What happens if you draw isosurfaces? Do they change? -michael On 1/7/07, Raúl Mera wrote: Dear all, Two things. First, I just written a small plugin that uses the program "reduce" to add hydrogens to a molecule or to a trajectory loaded in Pymol.(since each frame of the trajectory is hydrogenated by reduce, I think that protonation states could vary between frames) This allow us to have a reliable protonation method in PyMOL, without having to save the structure as PDB and hydrogenate with another app, and using an open-source (as far as I know) and easy to install application. Since I don't have any website right now, I will try to make it available from the Pymol Wiki. If you want the plugin right now, just e-mail me. The other thing is a doubt in using the APBS Tools. When I use it to calculate electrostatics potentialsof a trajectory (but the PQR is made by PDB2PQR from a PDB made with PyMOL, i.e, only from the first snapshot) I get a .dx map that I think has the potentials only for the first frame. When I display the potential surface in the trajectory, the potentials seems to change between frames, which I wouldn't expect since I think that the calculation was performed only for the first frame. My doubt is: Are these changes alleatory due to a change of the structure's position changes on the grid, or they have some significance?, if the latter, what significance? (maybe the changes are produced by the motion of polar groups?) Thanks in advance, Raul __ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! Regístrate ya - http://correo.espanol.yahoo.com/ - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net
[PyMOL] New plugin and Doubt with APBS Tools
Dear all, Two things. First, I just written a small plugin that uses the program "reduce" to add hydrogens to a molecule or to a trajectory loaded in Pymol.(since each frame of the trajectory is hydrogenated by reduce, I think that protonation states could vary between frames) This allow us to have a reliable protonation method in PyMOL, without having to save the structure as PDB and hydrogenate with another app, and using an open-source (as far as I know) and easy to install application. Since I don't have any website right now, I will try to make it available from the Pymol Wiki. If you want the plugin right now, just e-mail me. The other thing is a doubt in using the APBS Tools. When I use it to calculate electrostatics potentialsof a trajectory (but the PQR is made by PDB2PQR from a PDB made with PyMOL, i.e, only from the first snapshot) I get a .dx map that I think has the potentials only for the first frame. When I display the potential surface in the trajectory, the potentials seems to change between frames, which I wouldn't expect since I think that the calculation was performed only for the first frame. My doubt is: Are these changes alleatory due to a change of the structure's position changes on the grid, or they have some significance?, if the latter, what significance? (maybe the changes are produced by the motion of polar groups?) Thanks in advance, Raul __ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! Regístrate ya - http://correo.espanol.yahoo.com/
