Jan, Perform the structure alignment after loading the structure and map:
load 1zziA_pbeq.pdb load 1zziA_pbeq.dx, 1zziA_map # add load target.pdb align 1zziA_pbeq////CA, target////CA matrix_copy 1zziA_pbeq, 1zziA_map # Then continue with the rest of your script. Cheers, Warren > -----Original Message----- > From: Jan Kosinski [mailto:k...@genesilico.pl] > Sent: Tuesday, April 28, 2009 8:03 AM > To: Carlos Huerta > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] rotating map > > I cannot do that, because the CHARMM-GUI server that I use > for calculating the electrostatic potential changes the > orientation of the input structures (I reported that to the authors). > > Cheers, > Janek > > Carlos Huerta wrote: > > Janek, > > > > You need to align your structure with the reference, then > re-calculate the electrostatic potentials. > > > > Sincerely, > > > > Carlos > > > > > >>>> Jan Kosinski <k...@genesilico.pl> 04/28/09 9:04 AM >>> > >>>> > > I am visualizing in PyMol electrostatic potential generated by PBEQ > > Solver from CHARMM-GUI at > > http://www.charmm-gui.org/?doc=input/pbeqsolver > > > > The maps loads and colors nicely with the following > commands suggested > > by the PBEQ Solver server: > > load 1zziA_pbeq.pdb > > load 1zziA_pbeq.dx, 1zziA_map > > show surface, 1zziA_pbeq > > ramp_new 1zziA_elvl, 1zziA_map,[-2,0,2] set surface_color, > 1zziA_elvl, > > 1zziA_pbeq set surface_solvent, 1, 1zziA_pbeq > > > > Now I want to fit my structure to some reference one using super or > > align commands. As expected, the map no longer works, I cannot > > re-generate the original coloring after fitting. I suppose > that I need > > to change the orientation of the map accordingly to the rotation of > > the structure. But... how to do that? Is it at all possible? > > > > Cheers, > > Janek > > > > > ---------------------------------------------------------------------- > > -------- Register Now & Save for Velocity, the Web Performance & > > Operations Conference from O'Reilly Media. Velocity features a full > > day of expert-led, hands-on workshops and two days of sessions from > > industry leaders in dedicated Performance & Operations tracks. Use > > code vel09scf and Save an extra 15% before 5/3. > > http://p.sf.net/sfu/velocityconf > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > > > > > -------------------------------------------------------------- > ---------------- > Register Now & Save for Velocity, the Web Performance & > Operations Conference from O'Reilly Media. Velocity features > a full day of expert-led, hands-on workshops and two days of > sessions from industry leaders in dedicated Performance & > Operations tracks. Use code vel09scf and Save an extra 15% > before 5/3. http://p.sf.net/sfu/velocityconf > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > ------------------------------------------------------------------------------ Register Now & Save for Velocity, the Web Performance & Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance & Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
