Re: [PyMOL] isosurface stays gray after using "surface_color" command and "rebuild"

[Fux S. (ID SIS) <sam...@id...>]

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/
sam...@id...

________________________________________
Von: Thomas Holder [tho...@sc...]
Gesendet: Mittwoch, 11. Januar 2017 17:07
An: Fux Samuel (ID SIS)
Cc: pym...@li...
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) <sam...@id...> 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.