From: Oliver Beckstein (oliver_at_biop.ox.ac.uk)
Date: Tue Feb 08 2005 - 15:28:30 CST

John,

> I just ran the test on an NVidia GeForce 6800GT under Linux and
> it worked fine so far. I've attached an example image of what I get
> when I load the PDB and DX file and render an MSMS surface colored
> by electrostatic potential with the color scale range set from -5 to 5
> and the color scale mode set to RWB. This is what you ought to be
> seeing when you do the steps you outlined below.

Yes, that looks familiar---I saw it once on my screen. Well, I'll keep
trying and run it on another machine to see if it's an issue with my
particular setup.

Thanks,
Oliver

>
> John
>
>
> On Tue, Feb 08, 2005 at 05:25:25PM +0000, Oliver Beckstein wrote:
> > John,
> >
> > thanks for looking into this. First off, I managed to get it working
> > _once_ and can't reproduce it. I describe the normal procedure below, and
> > also what made it work once.
> >
> > > I'm able to load and display your potential map with no trouble
> > >on a test machine here, so VMD itself appears to be working fine
> > >with this data, so the only question that remains is what the story
> > >is with your video board.
> >
> > Ok, that's good to know, so the potential map isn't off the protein as
> > Axel suggested as an alternative source of error.
> >
> > >I get nice coloring if I set the color scale data range in the
> > >"trajectory" tab to range from -5 to 5. With the full-range (default) I
> > >get a mostly white surface.
> >
> > I get solid black. Just to check that I'm not doing something REALLY
> > stupid I describe what I do:
> >
> > 0) start vmd 1.8.3b1
> > 1) File > New Molecule: Load 7AHL.pdb
> > (the apbs calculation was done on 7AHL.pqr but some of the hydrogens
> > are in the wrong place and msms chockes on it so I just use the
> > one with polar hydrogens; it superimposes with the all-hydrogen
> > structure)
> > 2) Load into 7AHL.pdb: 7AHL.dx
> > 3) Graphics > Representations:
> > Drawing method: MSMS
> > Coloring Method: Volume
> > (now color is 'Volume 0' where
> > 0: 7AHL.dx: regular positions regular grid)
> > The MSMS surface is black.
> > 4) in Representations: [Trajectory]
> > Color scale data range:
> > -5 5 set
> > ... still black.
> >
> > >I don't have time right this moment, but I'll give it a sping on a few
> > >of our NVidia cards here and see if they behave differently at all.
> > >
> > >Do you get anything from the VolumeSlice representation, or is it
> > >solid black also?
> >
> > VolumeSlice is pitch-black, too (range set to -5 -> 5).
> >
> > I also tried another density file in plt format:
> > vmd > Info) Analyzing Volume...
> > Info) Grid size: 46x46x78 (2 MB)
> > Info) Total voxels: 165048
> > Info) Min: 0.000000 Max: 11.555668 Range: 11.555668
> >
> > This gives a coloured slice and I can colour the surface of the other
> > protein; the regions not in the density are black (as in Axel's image).
> >
> > After loading the plt I switched the volume rendering back to my dx map
> > and suddenly the black surface become coloured, just as it should be.
> > Setting limits, changing colour scale--- all worked beautifully.
> >
> > Then I tried to reproduce this, starting vmd again... and never got it to
> > work again (writing after about 10 attempts).
> >
> > I can colour the plt volume slice by volume (using the plt density) and I
> > get a nice rendering; when coloured by the dx set it gives a strange
> > washed out (?) image of the plt file (hard to describe). If I draw the dx
> > data set as a slice it is black, regardless if volume-coloured by the dx
> > or plt.
> >
> >
> > Anything else I could try/look at? I listed parts of xorg.conf, the X
> > server log file and output from glxinfo.
> >
> > Best wishes,
> > Oliver
> >
> > ---------
> >
> > The (boring) entry from /etc/X11/xorg.conf:
> > ---------------------------------------------------------
> > Section "Device"
> > Identifier "NVIDIA GeForce 4 (accelerated)"
> > Driver "nvidia"
> > VendorName "NVIDIA"
> > BoardName "Quadro 4 900XGL"
> > EndSection
> > ---------------------------------------------------------
> >
> > >From /var/log/Xorg.0.log :
> > ------------------------------------------------------------
> > (--) PCI:*(1:0:0) nVidia Corporation NV25GL [Quadro4 900 XGL] rev 163, Mem
> > @ 0xf4000000/24, 0xe0000000/27, 0xe8000000/19
> > .....
> > (II) Loading /usr/X11R6/lib/modules/extensions/libglx.so
> > (II) Module glx: vendor="NVIDIA Corporation"
> > compiled for 4.0.2, module version = 1.0.6629
> > Module class: XFree86 Server Extension
> > ABI class: XFree86 Server Extension, version 0.1
> > (II) Loading extension GLX
> > (II) LoadModule: "nvidia"
> > (II) Loading /usr/X11R6/lib/modules/drivers/nvidia_drv.o
> > (II) Module nvidia: vendor="NVIDIA Corporation"
> > compiled for 4.0.2, module version = 1.0.6629
> > Module class: XFree86 Video Driver
> > ....
> > (II) NVIDIA X Driver 1.0-6629 Wed Nov 3 13:14:07 PST 2004
> > (II) NVIDIA Unified Driver for all NVIDIA GPUs
> > (II) Primary Device is: PCI 01:00:0
> > (--) Assigning device section with no busID to primary device
> > (--) Chipset NVIDIA GPU found
> > ....
> > (II) NVIDIA(0): Setting mode "1280x1024"
> > (II) Loading extension NV-GLX
> > (II) NVIDIA(0): NVIDIA 3D Acceleration Architecture Initialized
> > (II) NVIDIA(0): Using the NVIDIA 2D acceleration architecture
> > (==) NVIDIA(0): Backing store disabled
> > (==) NVIDIA(0): Silken mouse enabled
> > (**) Option "dpms"
> > (**) NVIDIA(0): DPMS enabled
> > (II) Loading extension NV-CONTROL
> > (==) RandR enabled
> > ---------------------------------------------------------------------
> >
> > >From glxinfo:
> > ---------------------------------------------------------------------
> > name of display: :0.0
> > display: :0 screen: 0
> > direct rendering: Yes
> > server glx vendor string: NVIDIA Corporation
> > server glx version string: 1.3
> > server glx extensions:
> > GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig,
> > GLX_SGIX_pbuffer, GLX_SGI_video_sync, GLX_SGI_swap_control,
> > GLX_ARB_multisample
> > client glx vendor string: NVIDIA Corporation
> > client glx version string: 1.3
> > client glx extensions:
> > GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_visual_info,
> > GLX_EXT_visual_rating, GLX_EXT_import_context, GLX_SGI_video_sync,
> > GLX_NV_swap_group, GLX_NV_video_out, GLX_SGIX_fbconfig,
> > GLX_SGIX_pbuffer,
> > GLX_SGI_swap_control, GLX_NV_float_buffer
> > GLX extensions:
> > GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig,
> > GLX_SGIX_pbuffer, GLX_SGI_video_sync, GLX_SGI_swap_control,
> > GLX_ARB_multisample, GLX_ARB_get_proc_address
> > OpenGL vendor string: NVIDIA Corporation
> > OpenGL renderer string: Quadro4 900 XGL/AGP/SSE
> > OpenGL version string: 1.5.2 NVIDIA 66.29
> > OpenGL extensions:
> > GL_ARB_depth_texture, GL_ARB_imaging, GL_ARB_multisample,
> > GL_ARB_multitexture, GL_ARB_occlusion_query, GL_ARB_point_parameters,
> > GL_ARB_point_sprite, GL_ARB_shadow, GL_ARB_shader_objects,
> > GL_ARB_shading_language_100, GL_ARB_texture_border_clamp,
> > GL_ARB_texture_compression, GL_ARB_texture_cube_map,
> > GL_ARB_texture_env_add, GL_ARB_texture_env_combine,
> > GL_ARB_texture_env_dot3, GL_ARB_texture_mirrored_repeat,
> > GL_ARB_texture_rectangle, GL_ARB_transpose_matrix,
> > GL_ARB_vertex_buffer_object, GL_ARB_vertex_program,
> > GL_ARB_vertex_shader,
> > GL_ARB_window_pos, GL_S3_s3tc, GL_EXT_texture_env_add, GL_EXT_abgr,
> > GL_EXT_bgra, GL_EXT_blend_color, GL_EXT_blend_minmax,
> > GL_EXT_blend_subtract, GL_EXT_compiled_vertex_array, GL_EXT_Cg_shader,
> > GL_EXT_draw_range_elements, GL_EXT_fog_coord,
> > GL_EXT_multi_draw_arrays,
> > GL_EXT_packed_pixels, GL_EXT_paletted_texture,
> > GL_EXT_pixel_buffer_object,
> > GL_EXT_point_parameters, GL_EXT_rescale_normal,
> > GL_EXT_secondary_color,
> > GL_EXT_separate_specular_color, GL_EXT_shadow_funcs,
> > GL_EXT_shared_texture_palette, GL_EXT_stencil_wrap, GL_EXT_texture3D,
> > GL_EXT_texture_compression_s3tc, GL_EXT_texture_cube_map,
> > GL_EXT_texture_edge_clamp, GL_EXT_texture_env_combine,
> > GL_EXT_texture_env_dot3, GL_EXT_texture_filter_anisotropic,
> > GL_EXT_texture_lod, GL_EXT_texture_lod_bias, GL_EXT_texture_object,
> > GL_EXT_vertex_array, GL_HP_occlusion_test, GL_IBM_rasterpos_clip,
> > GL_IBM_texture_mirrored_repeat, GL_KTX_buffer_region,
> > GL_NV_blend_square,
> > GL_NV_copy_depth_to_color, GL_NV_depth_clamp, GL_NV_fence,
> > GL_NV_fog_distance, GL_NV_light_max_exponent,
> > GL_NV_multisample_filter_hint, GL_NV_occlusion_query,
> > GL_NV_packed_depth_stencil, GL_NV_pixel_data_range,
> > GL_NV_point_sprite,
> > GL_NV_register_combiners, GL_NV_register_combiners2,
> > GL_NV_texgen_reflection, GL_NV_texture_compression_vtc,
> > GL_NV_texture_env_combine4, GL_NV_texture_rectangle,
> > GL_NV_texture_shader,
> > GL_NV_texture_shader2, GL_NV_texture_shader3,
> > GL_NV_vertex_array_range,
> > GL_NV_vertex_array_range2, GL_NV_vertex_program,
> > GL_NV_vertex_program1_1,
> > GL_SGIS_generate_mipmap, GL_SGIS_multitexture, GL_SGIS_texture_lod,
> > GL_SGIX_depth_texture, GL_SGIX_shadow, GL_SUN_slice_accum
> > glu version: 1.3
> > glu extensions:
> > GLU_EXT_nurbs_tessellator, GLU_EXT_object_space_tess
> >
> > ....
> > --------------------------------------------------------------------
> >
> >
> > >
> > > John
> > >
> > >On Mon, Feb 07, 2005 at 06:23:35PM +0000, Oliver Beckstein wrote:
> > >>John,
> > >>
> > >>please find the files in
> > >>http://indigo1.biop.ox.ac.uk/oliver/download/Outgoing/vmd/VolumeShading/
> > >>
> > >>The dx file is bzipped, and I put the pdb/pqr files there as well. They
> > >>were generated from a pqr file from pdb2pqr with the apbs plugin at
> > >>default settings.
> > >>
> > >>I haven't posted this one to the list but the rest of the discussion
> > >>should go back there, I think.
> > >>
> > >>Btw, _is_ GL shading necessary for volume/slice shading to work? Just
> > >>wondering because my machine at home currently only uses the Mesa driver,
> > >>and shows the surfaces in white (volume shading) or no volume slices at
> > >>all. I used the RGB scale for Graphics > Colour > Surface.
> > >>
> > >>Best wishes,
> > >>Oliver
> > >>
> > >>On Mon, 7 Feb 2005, John Stone wrote:
> > >>
> > >>>
> > >>>Oliver,
> > >>> I'd have guessed that the value range was the issue, but if you're
> > >>>using the Red White Blue color scale, there shouldn't be any pixel
> > >>>values that are black at all, so that points to some other issue
> > >>>causing this difficulty. Can you send me a copy of the DX file in
> > >>>question so I can have a look at it?
> > >>>
> > >>>Thanks,
> > >>> John Stone
> > >>> vmd_at_ks.uiuc.edu
> > >>>
> > >>>On Mon, Feb 07, 2005 at 04:58:50PM +0000, Oliver Beckstein wrote:
> > >>>>John,
> > >>>>
> > >>>>> I assume you've got the latest NVidia drivers installed for your
> > >>>>>video board?
> > >>>>
> > >>>>Yes, 1.0-6629 is the latest one.
> > >>>>
> > >>>>>What resolution is the potential map you're trying to load?
> > >>>>
> > >>>>129x129x129
> > >>>>
> > >>>>Info) Analyzing Volume...
> > >>>>Info) Grid size: 129x129x129 (32 MB)
> > >>>>Info) Total voxels: 2146689
> > >>>>Info) Min: -747.528870 Max: 633.049377 Range: 1380.578247
> > >>>>Info) Computing volume gradient map for smooth shading
> > >>>>Info) Added volume data, name=pot.dx : regular positions regular
> > >>>>connections
> > >>>>
> > >>>>Hmm---is it perhaps a problem with the range of values?
> > >>>>
> > >>>>Any help is appreciated,
> > >>>>Oliver
> > >>>>
> > >>>>>On Mon, Feb 07, 2005 at 04:03:34PM +0000, Oliver Beckstein wrote:
> > >>>>>>Hi,
> > >>>>>>
> > >>>>>>I would like to create grasp-like electrostatic maps. I produced a
> > >>>>>>pot.dx
> > >>>>>>potential map with apbs and tried to colour a 'surf' or 'msms' surface
> > >>>>>>using the new volume colouring feature. However, the surface stays
> > >>>>>>uniformly black although I would expect some variation along
> > >>>>>>red-white-blue (I think this is set with the colour scale.)
> > >>>>>>
> > >>>>>>Also, volume slice gives me a black surface. The iso contour
> > >>>>>>representation works as expected, though.
> > >>>>>>
> > >>>>>>Do I need OpenGL shading for this to work?
> > >>>>>>
> > >>>>>>When I try Display>Render Mode>GLSL I get "Warning) OpenGL
> > >>>>>>Programmable
> > >>>>>>Shading not available."
> > >>>>>>
> > >>>>>>(I have
> > >>>>>>
> > >>>>>>VMD 1.8.3b1
> > >>>>>>
> > >>>>>>Info) OpenGL renderer: Quadro4 900 XGL/AGP/SSE
> > >>>>>>Info) Features: STENCIL MSAA(4) RN MDE CVA MTX TCM PP PS GLSL SHO
> > >>>>>>SHV
> > >>>>>>Info) OpenGL Programmable shading is NOT available.
> > >>>>>>Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
> > >>>>>>
> > >>>>>>Fedora Core 3, xorg (nothing special in xorg.conf),
> > >>>>>>NVIDIA-Linux-x86-1.0-6629 )
> > >>>>>>
> > >>>>>>Thanks,
> > >>>>>>Oliver
> > >>>>>>
> > >>>>>>--
> > >>>>>>Oliver Beckstein * oliver_at_biop.ox.ac.uk
> > >>>>>> http://sansom.biop.ox.ac.uk/oliver/
> > >>>>>
> > >>>>>--
> > >>>>>NIH Resource for Macromolecular Modeling and Bioinformatics
> > >>>>>Beckman Institute for Advanced Science and Technology
> > >>>>>University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > >>>>>Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > >>>>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > >>>>>
> > >>>>>
> > >>>>
> > >>>>--
> > >>>>Oliver Beckstein * oliver_at_biop.ox.ac.uk
> > >>>> http://sansom.biop.ox.ac.uk/oliver/
> > >>>
> > >>>--
> > >>>NIH Resource for Macromolecular Modeling and Bioinformatics
> > >>>Beckman Institute for Advanced Science and Technology
> > >>>University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > >>>Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > >>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > >>>
> > >>>
> > >>
> > >>--
> > >>Oliver Beckstein * oliver_at_biop.ox.ac.uk
> > >> http://sansom.biop.ox.ac.uk/oliver/
> > >
> > >--
> > >NIH Resource for Macromolecular Modeling and Bioinformatics
> > >Beckman Institute for Advanced Science and Technology
> > >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > >
> > >
> >
> > --
> > Oliver Beckstein * oliver_at_biop.ox.ac.uk
> > http://sansom.biop.ox.ac.uk/oliver/
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>

-- 
Oliver Beckstein * oliver_at_biop.ox.ac.uk
 http://sansom.biop.ox.ac.uk/oliver/