Re: [PyMOL] Slice
Dear Thomas, It’s phimap.cube file. ( .cube is an extension). These cube files are from Delphi. ( Poisson Boltzmann solver). Thank you , Best Regards Divya Get Outlook for iOS<https://aka.ms/o0ukef> From: Thomas Holder Sent: Friday, August 17, 2018 4:51 AM To: Divya Kaur Matta Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Slice Hi Divya, I can confirm that slices don't work properly with some map formats (those which define a transformation matrix). What's the file format (file extension) of your map? Cheers, Thomas > On Aug 15, 2018, at 7:38 PM, Divya Kaur Matta > wrote: > > Dear all, > > > I would like to use the "Isomesh" and "Slice" command for the protein I am > working on to get the electrostatic potential map of that protein. For that , > it requires map. I have got Delphi map for that. When I use the commands > below, I got the mesh that aligns with the atoms of the pdb, however for > slice, it is not aligned with the atoms. I would like to have a slice plane > for my protein. > > > For isomesh, > > isomesh map_n20, phimap, -20.0 ; color red, map_n20 > > isomesh map_p20, phimap, 20.0 ; color blue, map_p20 > > For slice, > > I did actions, show slice(default) > > Please find attached images for the slice I got. > > > Thank you! > > Best Regards, > > Divya K. Matta > Ph.D. Student in Chemistry -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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] Slice
Dear Thomas , Thank you so much for your suggestion. I will try this. I appreciate your help. Best Regards Divya Get Outlook for iOS<https://aka.ms/o0ukef> From: Thomas Holder Sent: Friday, August 17, 2018 11:05 AM To: Divya Kaur Matta Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Slice Hi Divya, Try to output a .phi file with delphi, that format should work fine with slices. In your delphi .param file: out(phi,file=phimap.phi,format=0) Cheers, Thomas > On Aug 17, 2018, at 4:28 PM, Divya Kaur Matta > wrote: > > Dear Thomas, > > It’s phimap.cube file. ( .cube is an extension). These cube files are from > Delphi. ( Poisson Boltzmann solver). > > Thank you , > > Best Regards > Divya > > Get Outlook for iOS > From: Thomas Holder > Sent: Friday, August 17, 2018 4:51 AM > To: Divya Kaur Matta > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Slice > > Hi Divya, > > I can confirm that slices don't work properly with some map formats (those > which define a transformation matrix). > > What's the file format (file extension) of your map? > > Cheers, > Thomas > > > On Aug 15, 2018, at 7:38 PM, Divya Kaur Matta > > wrote: > > > > Dear all, > > > > > > I would like to use the "Isomesh" and "Slice" command for the protein I am > > working on to get the electrostatic potential map of that protein. For that > > , it requires map. I have got Delphi map for that. When I use the commands > > below, I got the mesh that aligns with the atoms of the pdb, however for > > slice, it is not aligned with the atoms. I would like to have a slice plane > > for my protein. > > > > > > For isomesh, > > > > isomesh map_n20, phimap, -20.0 ; color red, map_n20 > > > > isomesh map_p20, phimap, 20.0 ; color blue, map_p20 > > > > For slice, > > > > I did actions, show slice(default) > > > > Please find attached images for the slice I got. > > > > > > Thank you! > > > > Best Regards, > > > > Divya K. Matta > > Ph.D. Student in Chemistry -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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] Slice
Hi Divya, Try to output a .phi file with delphi, that format should work fine with slices. In your delphi .param file: out(phi,file=phimap.phi,format=0) Cheers, Thomas > On Aug 17, 2018, at 4:28 PM, Divya Kaur Matta > wrote: > > Dear Thomas, > > It’s phimap.cube file. ( .cube is an extension). These cube files are from > Delphi. ( Poisson Boltzmann solver). > > Thank you , > > Best Regards > Divya > > Get Outlook for iOS > From: Thomas Holder > Sent: Friday, August 17, 2018 4:51 AM > To: Divya Kaur Matta > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Slice > > Hi Divya, > > I can confirm that slices don't work properly with some map formats (those > which define a transformation matrix). > > What's the file format (file extension) of your map? > > Cheers, > Thomas > > > On Aug 15, 2018, at 7:38 PM, Divya Kaur Matta > > wrote: > > > > Dear all, > > > > > > I would like to use the "Isomesh" and "Slice" command for the protein I am > > working on to get the electrostatic potential map of that protein. For that > > , it requires map. I have got Delphi map for that. When I use the commands > > below, I got the mesh that aligns with the atoms of the pdb, however for > > slice, it is not aligned with the atoms. I would like to have a slice plane > > for my protein. > > > > > > For isomesh, > > > > isomesh map_n20, phimap, -20.0 ; color red, map_n20 > > > > isomesh map_p20, phimap, 20.0 ; color blue, map_p20 > > > > For slice, > > > > I did actions, show slice(default) > > > > Please find attached images for the slice I got. > > > > > > Thank you! > > > > Best Regards, > > > > Divya K. Matta > > Ph.D. Student in Chemistry -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ 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] Slice
Hi Divya, I can confirm that slices don't work properly with some map formats (those which define a transformation matrix). What's the file format (file extension) of your map? Cheers, Thomas > On Aug 15, 2018, at 7:38 PM, Divya Kaur Matta > wrote: > > Dear all, > > > I would like to use the "Isomesh" and "Slice" command for the protein I am > working on to get the electrostatic potential map of that protein. For that , > it requires map. I have got Delphi map for that. When I use the commands > below, I got the mesh that aligns with the atoms of the pdb, however for > slice, it is not aligned with the atoms. I would like to have a slice plane > for my protein. > > > For isomesh, > > isomesh map_n20, phimap, -20.0 ; color red, map_n20 > > isomesh map_p20, phimap, 20.0 ; color blue, map_p20 > > For slice, > > I did actions, show slice(default) > > Please find attached images for the slice I got. > > > Thank you! > > Best Regards, > > Divya K. Matta > Ph.D. Student in Chemistry -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ 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] Slice
Dear all, I would like to use the "Isomesh" and "Slice" command for the protein I am working on to get the electrostatic potential map of that protein. For that , it requires map. I have got Delphi map for that. When I use the commands below, I got the mesh that aligns with the atoms of the pdb, however for slice, it is not aligned with the atoms. I would like to have a slice plane for my protein. For isomesh, isomesh map_n20, phimap, -20.0 ; color red, map_n20 isomesh map_p20, phimap, 20.0 ; color blue, map_p20 For slice, I did actions, show slice(default) Please find attached images for the slice I got. Thank you! Best Regards, Divya K. Matta Ph.D. Student in Chemistry -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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
