June 2003 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Chimera - Dock grid
by Thomas Goddard 20 Jun '03

20 Jun '03

Hi Joel, The voldata.tar.gz file had a bug. I forgot to do byte swapping on the grid values. So it works on SGI and Mac or on Linux and Windows, but not both. I fixed this problem. The new code is at: http://www.cgl.ucsf.edu/home/goddard/voldata.tar.gz Tom

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Chimera - Dock grid
by chimera-users＠cgl.ucsf.edu 20 Jun '03

20 Jun '03

Hi there, I'm quite impressed with chimera and its dock functionality. My query is about dock grid. I can't find any documentation about this ie what the values and their ranges represent. Also I can't seem to turn them off once they are on. And not to be too ungrateful different colours would be handy as well...how can I change those? While I'm at it is there a delete molecule button? Thanks for your help in advance joel -- ________________________________________ Joel Tyndall, PhD Research Officer http://www.imb.uq.edu.au Institute for Molecular Bioscience incorporating Centre for Drug Design and Development Centre for Cellular and Molecular Biology The University of Queensland Brisbane Australia 4072 Tel: +61 7 3346 2988 Fax: +61 7 3346 2101 email: J.Tyndall(a)imb.uq.edu.au

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denbsity maps
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi, I am using chimera to make some pictures of a model docked into a low resolution electron density map. Is there a way to make the mesh lines representing the electron density thicker? Also is it possible to have a cubic grid rather than triangles? Thankyou very much for your help. Suzanne Brewerton University of Cambridge --

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writing Mol2 format
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi David, Writing out Mol2 format can in principle be done, but there are a few caveats. If the original format is Mol2, the original information could be retained and written back out. I don't know how simple/hard this would be to implement (feel free to chime in, other members of the team). When the original format is not Mol2, there is less information in the molecule data than is needed to write the file. Chimera uses a fairly rich set of atom types, but there is still not a one-to-one relationship with all Mol2 types. One would need to create a mapping between the types. Also, I believe Chimera currently knows connectivity but not bond orders, and does not retain any point charge information. The online Chimera Programmer's Guide actually includes an example of code required to write out a mol2 file. I had forgotten about this when visiting your office earlier. It discusses a mapping between atom types (if you use this, you should examine this mapping and make sure it works the way you think it should). The example code writes out all bonds as single. Check it out: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html click the "Examples" link and then "Chimera's Object Model" This example is "writeMol2.py" If you have a molecule open in Chimera, you can view the type assignments using Actions... Label... IDATM type (version 1.1700). A listing/explanation of Chimera types can be seen at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html Best, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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denbsity maps
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi, I am using chimera to make some pictures of a model docked into a low resolution electron density map. Is there a way to make the mesh lines representing the electron density thicker? Also is it possible to have a cubic grid rather than triangles? Thankyou very much for your help. Suzanne Brewerton University of Cambridge --

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Writing to mol2
by chimera-users＠cgl.ucsf.edu 18 Jun '03

18 Jun '03

Hi, I'm one of your "neighbors" working in the Shoichet lab for the summer. I think it'd be neat if you could output in mol2 format rather than just pdb format, especially if the input is in mol2. Is this in the works? Has it already been done? Is it easy to do? David Minh

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Chimera & dock grids
by chimera-users＠cgl.ucsf.edu 18 Jun '03

18 Jun '03

Dear Dr. Tyndall, Thanks for your interest - DOCKgrid is indeed undocumented, partly because we have a much more advanced extension for viewing 3D data sets, Volume Viewer. This would let you have multiple contour surfaces or transparent solids in colors of your choosing, with interactively adjustable thresholds. The current hitch is that the DOCK grid formats have not yet been added to the Volume Viewer extension. We are actively looking into this and hope to incorporate it soon (we will let you know when this happens). I believe the values are directly those stored in the grid files, which (for dock 4 at least) are described in http://dock.compbio.ucsf.edu/dock4/html/Manual.1c.html#pgfId=850 The VDW repulsion, VDW attraction, and electrostatic grid values are described in equation 9 (all three are in the *.nrg grid). These are not in energy units until multiplied by ligand atom parameters. I believe the color choices in DOCKGrid are red and red. Display with Volume Viewer should be a vast improvement. To close molecules and also these contour surfaces, one way is to open the Model Panel (Tools... Inspectors... Model Panel in version 1.1700). In the Model Panel, choose the model(s) you want to close on the left side, then click "close" on the right side (not the Model Panel Close button). Unfortunately the contour surfaces created by DOCKgrid are each VRML files without an informative title, so it may be hard to tell which is which. If you only have one, of course, it will be obvious. I hope this helps! Best regards, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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Re: Chimera graphics card requirements
by chimera-users＠cgl.ucsf.edu 10 Jun '03

10 Jun '03

Hi Jim, I think Chimera will start without an OpenGL stencil buffer. But the outline highlighting of selected atoms/bonds/... will not work. Fill mode highlighting settable with Favorites/Preferences/General/ Selection highlight method will work. With a Quadro4 700 XGL on Linux you should definitely have a stencil buffer available. Below is the output of "glxinfo -t" on my Linux system with Quadro4 500 graphics. It shows half the visuals have 8 bit stencil buffer. It shows I am using the Nvidia 4191 driver OpenGL version string: 1.4.0 NVIDIA 41.91 Check the OpenGL version string on your machine to make sure you are using the Nvidia driver and not Mesa (software opengl). Tom $ glxinfo -t 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 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_SGIX_swap_group, GLX_SGIX_swap_barrier, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_NV_float_buffer GLX extensions: GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_ARB_get_proc_address OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: Quadro4 500 GoGL/AGP/SSE2 OpenGL version string: 1.4.0 NVIDIA 41.91 OpenGL extensions: GL_ARB_imaging, GL_ARB_multitexture, GL_ARB_point_parameters, 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_transpose_matrix, GL_ARB_vertex_program, GL_ARB_window_pos, GL_S3_s3tc, GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color, GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_clip_volume_hint, GL_EXT_compiled_vertex_array, GL_EXT_draw_range_elements, GL_EXT_fog_coord, GL_EXT_multi_draw_arrays, GL_EXT_packed_pixels, GL_EXT_paletted_texture, GL_EXT_point_parameters, GL_EXT_rescale_normal, GL_EXT_secondary_color, GL_EXT_separate_specular_color, GL_EXT_shared_texture_palette, GL_EXT_stencil_wrap, GL_EXT_texture_compression_s3tc, GL_EXT_texture_cube_map, GL_EXT_texture_edge_clamp, GL_EXT_texture_env_add, 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_IBM_texture_mirrored_repeat, GL_KTX_buffer_region, GL_NV_blend_square, GL_NV_fence, GL_NV_fog_distance, GL_NV_light_max_exponent, GL_NV_packed_depth_stencil, GL_NV_pixel_data_range, GL_NV_point_sprite, GL_NV_register_combiners, GL_NV_texgen_reflection, GL_NV_texture_env_combine4, GL_NV_texture_rectangle, GL_NV_vertex_array_range, GL_NV_vertex_array_range2, GL_NV_vertex_program, GL_NV_vertex_program1_1, GL_NVX_ycrcb, GL_SGIS_generate_mipmap, GL_SGIS_multitexture, GL_SGIS_texture_lod glu version: 1.3 glu extensions: GLU_EXT_nurbs_tessellator, GLU_EXT_object_space_tess Vis Vis Visual Trans buff lev render DB ste r g b a aux dep ste accum buffers MS MS ID Depth Type parent size el type reo sz sz sz sz buf th ncl r g b a num bufs ---------------------------------------------------------------------------------------------------- 0x21 24 TrueColor 0 32 0 rgba 1 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x22 24 DirectColor 0 32 0 rgba 1 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x23 24 TrueColor 0 32 0 rgba 1 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x24 24 TrueColor 0 32 0 rgba 0 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x25 24 TrueColor 0 32 0 rgba 0 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x26 24 TrueColor 0 32 0 rgba 1 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x27 24 TrueColor 0 32 0 rgba 1 0 8 8 8 8 0 0 0 16 16 16 16 0 0 0x28 24 TrueColor 0 32 0 rgba 0 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x29 24 TrueColor 0 32 0 rgba 0 0 8 8 8 8 0 0 0 16 16 16 16 0 0 0x2a 24 DirectColor 0 32 0 rgba 1 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x2b 24 DirectColor 0 32 0 rgba 0 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x2c 24 DirectColor 0 32 0 rgba 0 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x2d 24 DirectColor 0 32 0 rgba 1 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x2e 24 DirectColor 0 32 0 rgba 1 0 8 8 8 8 0 0 0 16 16 16 16 0 0 0x2f 24 DirectColor 0 32 0 rgba 0 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x30 24 DirectColor 0 32 0 rgba 0 0 8 8 8 8 0 0 0 16 16 16 16 0 0 > From: Jim Procter <procter(a)zbh.uni-hamburg.de> > Reply-To: procter(a)zbh.uni-hamburg.de > Organization: Zentrum Bioinformatik Hamburg > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Chimera graphics card requirements > Date: Tue, 10 Jun 2003 10:53:20 +0200 > > Hi. I'm sorry to bother you again - particularly with some trivial hardware > question, but I've been wondering about the minimum specification of OpenGL > graphics driver needed for Chimera. > > We have Quadro4 700 XGL/AGP/SSE2 drivers for our linux-installations, on what > I would expect to be fairly high-end PCs. There doesn't seem to be any way to > force these drivers to generate a stencil buffer - is this what other people > have found ? > > Thanks. > Jim

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Chimera-users June 2003