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.

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

2017-01-11 Thread Thomas Holder 
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] Xquartz/pymol issues OSX Sierra: rotation stops after a few milliseconds

2017-01-11 Thread hari jayaram 
Sorry to post back in.

As I posted yesterday ,  I have been trying to get pymol working on a
Macbook Air ( and MacBook Pro since yesterday ) and am now convinced the
X11 apps freezing problem is real and recurs frequently.

While rotating a molecule the X session stops responding , the window close
- window open-window minimize , red yellow green buttons gray out and then
the whole session freezes

I see this behavior on two machines I have tried using since my original
machine where everything was working but with an earlier brew installed
pymol ( 1.7.2 I think ) bit the dust.

IS anyone else seeing this with 1.8.2.1 and OSX?

Thanks
hari





I have used homebrew to install pymol version 1.8.2.1

On Tue, Jan 10, 2017 at 7:02 AM hari jayaram  wrote:

Hello All
Sorry for that post. The problem got fixed by a restart.
I failed to follow the unwritten rule of "non-Linux computers" :-) When in
doubt---restart

After a restart I tried pymol with a new user profile and it worked very
smoothly
I tried back with my migrated original account ...and the buttery smooth
rotation returnedPhew :-)

Sorry for the confusion
Thanks
Hari




On Tue, Jan 10, 2017 at 6:49 AM hari jayaram  wrote:

Hi ,
I was happily using brew installed pymol 1.7.6  on my Macbook Pro (running
OSX Sierra) and then had a hardware failure.

I switched computers to MacBook Air running the same version of OSX (Sierra
10.12.2 ) and Xquartz (2.7.11) and now pymol ( and coot and other X11 using
applications) refuses to function with smooth molecule rotation on even a
30kDa protein.

I know the Macbook Airs are not that underpowered and am wondering how to
troubleshoot the lack of smooth rotation.

I have tried:
Reinstalling pymol (now running 1.8)
Reinstalling Xquartz ( still running 2.7.11)
Using an external mouse


ANd still have rotation that gets stuck. It starts rotating smoothly and
then locks up. I can see the Mac red/yello/green circles go gray like X11
is sleeping when this happens . It resumes after a second and rotation
cotinues .

Looking for others having the same issue does not pull up anything. I can
get smooth rotation in Chimera and Cuemol2 on this new laptop so it seems
to be a Pymol(Coot) X11/Xquartz issue that I dont know how to fix.

Any ideas or help would be greatly appreciated since its two weeks till my
faithful computer returns from a hardware fix.

Thanks
Hari
--
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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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