RE: [PyMOL] Rotation of maps when aligning
Hi Tsjerk > Another (temporary) solution, which shouldn't be too hard to > implement, > would be the ability of 'glueing' the colors to the object. That is, > bind the color for each atom in the object, originating from > the map, to > that atom. That's not quite enough. The surface colors are defined by the map in this case, not by the atom. This means that the color may vary, even within areas that "belongs" to the same atom. > Brings me to a question. Is it currently possible to request > the color a > specific atom has? That would also make it possible to implement this > using python. Try iterate , print color to extract colors, and alter , color= to set colors. I don't know how color numbering works :-) Cheers, Esben > > Cheers, > > Tsjerk > > Warren DeLano wrote: > > >Esben, > > > > You've identified the only good workaround at present. > This is a > >high-priority need that should be addressed in the next couple of > >months as the internal matrix code in overhauled. My > apologies for the > >inconvenience. > > > >Cheers, > >Warren > > > >(PS. It is possible to transform the map, but you would > need the full > >matrix in order to do it, and PyMOL doesn't currently output > the matrix > >when it performs an alignment.) > > > >-- > >mailto:war...@delanoscientific.com > >Warren L. DeLano, Ph.D. > >Principal Scientist > >DeLano Scientific LLC > >Voice (650)-346-1154 > >Fax (650)-593-4020 > > > > > > > > > >>-Original Message- > >>From: pymol-users-ad...@lists.sourceforge.net > >>[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > >>EPF (Esben Peter Friis) > >>Sent: Tuesday, May 11, 2004 12:16 PM > >>To: pymol-users@lists.sourceforge.net > >>Subject: [PyMOL] Rotation of maps when aligning > >> > >> > >> > >>Hi PyMOLers > >> > >>I have a bunch of structures, for which I have calculated > >>electrostatic potential maps (using Gromacs and MEAD). I can > >>easily load the structures and corresponding maps into PyMOL > >>and display a color coded surface. But when I try to align > >>the structures, only the atomic coordinates are transformed - > >>the electrostatic maps remain in their original orientations. > >>As PyMOL update the surfaces after the alignment, the > >>resulting surface colors are completely wrong. Doing things > >>in another order doesn't help. > >> > >>As far as I can see from a posting from March 3rd (by John > >>Eksterowicz), the problem is exactly the same for a density map. > >> > >>In my case, the workaround is to align all the structures > >>before I do the electrostatic calculation - but it would be > >>better if the maps could be assigned to the coordinate system > >>of a structure. In this way, the maps would still be vaild > >>after a 3D-alignment. Is there a way to do this? > >> > >> > >>Best regards > >> > >>Esben > >> > >> > >> > >>--- > >>This SF.Net email is sponsored by Sleepycat Software Learn > >>developer strategies Cisco, Motorola, Ericsson & Lucent use > >>to deliver higher performing products faster, at low TCO. > >>http://www.sleepycat.com/telcomwpreg.php?From=dnemail3 > >>___ > >>PyMOL-users mailing list > >>PyMOL-users@lists.sourceforge.net > >>https://lists.sourceforge.net/lists/listinfo/pymol-users > >> > >> > >> > > > > > > > > > >--- > >This SF.Net email is sponsored by Sleepycat Software > >Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to > >deliver higher performing products faster, at low TCO. > >http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3 > >___ > >PyMOL-users mailing list > >PyMOL-users@lists.sourceforge.net > >https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > -- > ~ > -- :) > -- :) Tsjerk A. Wassenaar, M.Sc. > -- :) Molecular Dynamics Group > -- :) Dept. of Biophysical Chemistry > -- :) University of Groningen > -- :) Nijenborgh 4 > -- :) 9747 AG Groningen > -- :) The Netherlands > -- :) > ~ > -- :) > -- :) Hi! I'm a .signature virus! > -- :) Copy me into your ~/.signature to help me spread! > -- :) > ~ > > > > > --- > This SF.Net email is sponsored by Sleepycat Software > Learn developer strategies Cisco, Motorola, Ericsson & Lucent > use to deliver higher performing products faster, at low TCO. > http://www.sleepycat.com/telcomwpreg.php?> From=osdnemail3 > > > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://list
Re: [PyMOL] Rotation of maps when aligning
Hi Warren, Another (temporary) solution, which shouldn't be too hard to implement, would be the ability of 'glueing' the colors to the object. That is, bind the color for each atom in the object, originating from the map, to that atom. Brings me to a question. Is it currently possible to request the color a specific atom has? That would also make it possible to implement this using python. Cheers, Tsjerk Warren DeLano wrote: Esben, You've identified the only good workaround at present. This is a high-priority need that should be addressed in the next couple of months as the internal matrix code in overhauled. My apologies for the inconvenience. Cheers, Warren (PS. It is possible to transform the map, but you would need the full matrix in order to do it, and PyMOL doesn't currently output the matrix when it performs an alignment.) -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of EPF (Esben Peter Friis) Sent: Tuesday, May 11, 2004 12:16 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Rotation of maps when aligning Hi PyMOLers I have a bunch of structures, for which I have calculated electrostatic potential maps (using Gromacs and MEAD). I can easily load the structures and corresponding maps into PyMOL and display a color coded surface. But when I try to align the structures, only the atomic coordinates are transformed - the electrostatic maps remain in their original orientations. As PyMOL update the surfaces after the alignment, the resulting surface colors are completely wrong. Doing things in another order doesn't help. As far as I can see from a posting from March 3rd (by John Eksterowicz), the problem is exactly the same for a density map. In my case, the workaround is to align all the structures before I do the electrostatic calculation - but it would be better if the maps could be assigned to the coordinate system of a structure. In this way, the maps would still be vaild after a 3D-alignment. Is there a way to do this? Best regards Esben --- This SF.Net email is sponsored by Sleepycat Software Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver higher performing products faster, at low TCO. http://www.sleepycat.com/telcomwpreg.php?From=dnemail3 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- This SF.Net email is sponsored by Sleepycat Software Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver higher performing products faster, at low TCO. http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- ~ -- :) -- :) Tsjerk A. Wassenaar, M.Sc. -- :) Molecular Dynamics Group -- :) Dept. of Biophysical Chemistry -- :) University of Groningen -- :) Nijenborgh 4 -- :) 9747 AG Groningen -- :) The Netherlands -- :) ~ -- :) -- :) Hi! I'm a .signature virus! -- :) Copy me into your ~/.signature to help me spread! -- :) ~
RE: [PyMOL] Rotation of maps when aligning
Esben, You've identified the only good workaround at present. This is a high-priority need that should be addressed in the next couple of months as the internal matrix code in overhauled. My apologies for the inconvenience. Cheers, Warren (PS. It is possible to transform the map, but you would need the full matrix in order to do it, and PyMOL doesn't currently output the matrix when it performs an alignment.) -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > EPF (Esben Peter Friis) > Sent: Tuesday, May 11, 2004 12:16 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Rotation of maps when aligning > > > > Hi PyMOLers > > I have a bunch of structures, for which I have calculated > electrostatic potential maps (using Gromacs and MEAD). I can > easily load the structures and corresponding maps into PyMOL > and display a color coded surface. But when I try to align > the structures, only the atomic coordinates are transformed - > the electrostatic maps remain in their original orientations. > As PyMOL update the surfaces after the alignment, the > resulting surface colors are completely wrong. Doing things > in another order doesn't help. > > As far as I can see from a posting from March 3rd (by John > Eksterowicz), the problem is exactly the same for a density map. > > In my case, the workaround is to align all the structures > before I do the electrostatic calculation - but it would be > better if the maps could be assigned to the coordinate system > of a structure. In this way, the maps would still be vaild > after a 3D-alignment. Is there a way to do this? > > > Best regards > > Esben > > > > --- > This SF.Net email is sponsored by Sleepycat Software Learn > developer strategies Cisco, Motorola, Ericsson & Lucent use > to deliver higher performing products faster, at low TCO. > http://www.sleepycat.com/telcomwpreg.php?From=dnemail3 > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
