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

2017-01-12 Thread Fux Samuel (ID SIS) 
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)  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)  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
___
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Re: [PyMOL] isosurface stays gray after using "surface_color" command and "rebuild"

2017-01-11 Thread Fux Samuel (ID SIS) 
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)  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)
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[PyMOL] isosurface stays gray after using "surface_color" command and "rebuild"

2017-01-11 Thread Fux Samuel (ID SIS) 
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
--
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