VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 11 2017 - 08:07:56 CST

Hi,
  This mailing list is for discussions that have some relationship
to VMD. If you're having PyMOL troubles, I would suggest posting your
questions on the PyMOL mailing list here:
  https://lists.sourceforge.net/lists/listinfo/pymol-users

If you have VMD-specific questions, you're welcome to post those to this list.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 11, 2017 at 01:18:39PM +0000, Fux Samuel (ID SIS) 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 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/