VMD-L Mailing List

From: Fux Samuel (ID SIS) (samuel.fux_at_id.ethz.ch)
Date: Wed Jan 11 2017 - 07:18:39 CST

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