Hi Thomas, I just installed PyMOL 1.8.4 and now coloring the isosurface with the ramp from the cube file works fine.
Thank you very much for your help. Best regards Samuel -- ETH Zurich, Dr. sc. ETH Samuel Fux High Performance Computing, Scientific IT Services WEC D 13, Weinbergstrasse 11, 8092 Zurich, Switzerland Phone +41 44 632 57 63, http://www.id.ethz.ch/ samuel....@id.ethz.ch ________________________________________ Von: Thomas Holder [thomas.hol...@schrodinger.com] Gesendet: Donnerstag, 12. Januar 2017 09:26 An: Fux Samuel (ID SIS) Cc: pymol-users@lists.sourceforge.net Betreff: Re: [PyMOL] isosurface stays gray after using "surface_color" command and "rebuild" Hi Samuel, Thanks for the data range output, it looks fine. I checked the version history and found a bug which was fixed in 1.7.6. Color ramps didn't take the transformation matrix on the map into account, but cube files typically have such a matrix. Any chance you can upgrade to PyMOL 1.7.6 or newer? Cheers, Thomas On 12 Jan 2017, at 08:18, Fux Samuel (ID SIS) <samuel....@id.ethz.ch> wrote: > Hi Thomas, > > thank you for your reply. Please find below the data range of densf: > > PyMOL>print(cmd.get_volume_histogram("densf", 0)) > [-149.1259765625, 17.788000106811523, -1.1102406978607178, 29.603145599365234] > Best regards > > Samuel > > -- > ETH Zurich, Dr. sc. ETH Samuel Fux > High Performance Computing, Scientific IT Services > WEC D 13, Weinbergstrasse 11, 8092 Zurich, Switzerland > Phone +41 44 632 57 63, http://www.id.ethz.ch/ > samuel....@id.ethz.ch > > ________________________________________ > Von: Thomas Holder [thomas.hol...@schrodinger.com] > Gesendet: Mittwoch, 11. Januar 2017 17:07 > An: Fux Samuel (ID SIS) > Cc: pymol-users@lists.sourceforge.net > Betreff: Re: [PyMOL] isosurface stays gray after using "surface_color" > command and "rebuild" > > Hi Samuel, > > What's the data range of the "densf" map? > You can query the [min, max, mean, stdev] with: > print(cmd.get_volume_histogram("densf", 0)) > > Does the color show up with "ray"? (That is independent of OpenGL > capabilities) > > Thanks, > Thomas > > On 11 Jan 2017, at 16:11, Fux Samuel (ID SIS) <samuel....@id.ethz.ch> wrote: > > > Hi all, > > > > I am using PyMOL 1.7.4 on a HPC cluster (with X11-forwarding). The graphics > > card (ATI) of my workstation supports OpenGL 1.4. > > > > I am trying to color an isosurface with a color ramp from a cube file. I > > use the following commands: > > > > load PhCH2-2Py2H.xyz > > hide everything > > show sticks > > show spheres > > set stick_radius, .06 > > set sphere_scale, .18 > > set sphere_scale, .10, elem H > > set bg_rgb=[1, 1, 1] > > set stick_quality, 50 > > set sphere_quality, 4 > > color gray50, elem C > > color red, elem O > > color slate, elem N > > color gray98, elem H > > set stick_color, black > > set ray_trace_mode, 1 > > set ray_texture, 2 > > set antialias, 3 > > set ambient, 0.5 > > set spec_count, 5 > > set shininess, 50 > > set specular, 1 > > set reflect, .1 > > set dash_gap, 0 > > set dash_color, black > > set dash_gap, .15 > > set dash_length, .05 > > set dash_round_ends, 0 > > set dash_radius, .05 > > set fog, off > > ray > > > > load PhCH2-2Py2H_inter_py-dens.cube, densf > > load PhCH2-2Py2H_inter_py-grad.cube, gradf > > > > preset.ball_and_stick(selection='all') > > isosurface gradpos, gradf, 0.50 > > ramp_new ramp1, densf, [-5.0,0.0,5.0], [red,green,blue] > > set surface_color, ramp1, gradpos > > set two_sided_lighting, value=1 > > set transparency, 0.30 > > set surface_quality, 1 > > > > rebuild > > > > turn z,45 > > turn y,-3 > > turn z,-2 > > > > png PhCH2-2Py2H_inter_b.png, width=400, height=300, dpi=100, ray=1 > > > > turn z,-45 > > turn y,3 > > turn z,2 > > turn z,40.0 > > turn x,25 > > turn y,30 > > > > png PhCH2-2Py2H_inter_a.png, width=400, height=300, dpi=100, ray=1 > > After the "rebuild" command, the isosurface just stays gray while the color > > ramp is shown correctly. Do you have any idea how this problem could be > > solved (is OpenGL2 required for coloring an isosurface) ? > > > > The cluster is running under CentOS 6.8, on my workstation I am running > > Ubuntu 16.04. > > > > If there is any additional information that I can provide, then please let > > me know. > > > > Best regards and thank you > > > > Samuel -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi _______________________________________________ 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
