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.
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