June 2011 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

5 7

Re: [Chimera-users] Display a spider volume data in a specific orientation
by Elaine Meng 08 May '14

08 May '14

Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor… > It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation. I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0 You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used. I'm CC-ing the chimera-users(a)cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 7, 2010, at 11:51 AM, Li, Zongli wrote: > Hi Elaine, > I have a spider volume data (or mrc density map) from which I got a > serious 2D projections. I have the Euler angles for each projection. > Is there a way in Chimera that I can use those Euler angles to > display the 3D spider volume data (or mrc density map) in a specific > orientation that corresponding to that 2D projection? > Thank you very much in advance. > Best, > Zongli > > **************************************** > Zongli Li, Ph.D. > > Howard Hughes Medical Institute > Department of Cell Biology > Harvard Medical School > C Building, Room 420B > 240 Longwood Avenue > Boston, MA 02115 > > Tel: 617-432-4095 (Office) > 617-432-4708 (EM Suite) > 617-432-4091 (Computer room) > Fax: 617-432-1144 > Email: zongli_li(a)hms.harvard.edu > *************************************** >

3 5

font size in pull-down menus
by Boaz Shaanan 09 Oct '13

09 Oct '13

Hi, Is there a way to change the font size of the pull-down menus? For some reason on the Windows (XP) v.1.5.1 they seem smaller to me. Nothing in terms of graphics (or my eyesight) has changed since I upgraded to 1.5.1 recently. Thanks, Boaz Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

2 1

color surface based on NMR Order parameters
by lalit.deshmukh＠huskymail.uconn.edu 08 Sep '11

08 Sep '11

Hello, I like the 'surface color ' feature in Chimera. I think, right now, the surface can be colored by radius, height, volume data and so on.. Is it also possible to color the surface based upon the NMR order parameters or intensity ratios (it will be an Excel file containing just two columns: residue numbers and the respective parameter values)? Or this can be done in some other way? Thanks in advance, Regards, Lalit Deshmukh, University of Connecticut Storrs, CT 06269

5 8

Not Responding
by Chad Junkermeier 05 Jul '11

05 Jul '11

Hello, I have been having strange behavior lately with opening coordinate files. I am using xyz format files with up to 500 atoms. When I tell Chimera to open one of these files the computer sits for a moment and then starts reporting that Chimera is "Not Responding." I have tried this on three different Mac computers, one using OS X 10.6.7 (iMac Core i7, 8 GB Ram, ATI Radeon HD 4850) with all of the latest updates, one using OS X 10.6.7 (iMac Core 2 Duo, 4 GB Ram, NVIDIA GeForce 9400), and one 3 or 4 year old Macbook that has (4GB RAM, and I don't know anything else). On each of these machines I have tried using a variety of different versions of your code, and I continually find that I have the same problem. I also just installed Chimera on a Windows XP machine and it has similar issues. The xyz files are the product of relaxing a graphene sheet in Quantum Espresso, and then copying and pasting the final configuration out of the QE output file into a xyz file. Here are a few of the things that puzzle me. First, if I place the input configuration of atoms into a xyz file, Chimera will read in the structures without any problems. The output xyz files work in VMD and in iMol. I thought that it might be an issue with the xyz data structure and transformed it to PBD and it still wouldn't load. I also wondered if it was an issue of too many decimal points (higher precision than the input file), but after reducing the number of decimal points of each coordinate on all of the atoms, it still wouldn't work. I have looked through some of the output files and there doesn't appear to be any weirdness in any of the files. Further complicating this issue is that sometimes, after if I let it sit for a while, the program magically starts working. Again, I have no problem opening other files. Does anyone have any ideas on what to do to fix this problem? Chad

2 2

Re: [Chimera-users] Stereo vision with Quadro 600
by William Joseph Allen 29 Jun '11

29 Jun '11

Hi Greg, I was finally able to figure out what I was doing wrong. On the Nvidia control panel, I was changing the following settings: Stereo - Enable: 'On' Stereo - Display mode: 'Generic active stereo (with NVIDIA 3D vision)' For only specific programs (VMD, MOE, Chimera). That worked for VMD and MOE, but not for Chimera. As soon as I made those settings global, I was able to use stereo in Chimera. There must be other programs, like python.exe or something, that must also be stereo-enabled for this setup to work. Thanks again for your help, William Allen On 6/28/11 10:38 AM, Greg Couch wrote: > So according to the wglinfo output, your driver is not configured for stereo. > Check out the st/ro column, it is always a '.' and there should be some 'y's. > So no OpenGL stereo program should work. I did try the 275.36 driver with our > Quadro FX 3700, and stereo did work, so it is unclear why stereo isn't working > for you. To confirm that the driver configuration is working, try one of the > passive stereo options for the "Stereo - Display mode" and rerun wglinfo (or > Chimera) to see if stereo is supported. You also might want to go over the > driver settings with a colleague to see if either of you can spot anything, > and if that doesn't work, try an earlier version of the driver. > > Good luck, > > Greg > > On 6/27/2011 3:01 PM, William Joseph Allen wrote: >> Hi Greg, Here are the results: Thanks for your help! >> >> ########## >> C:\Users\William\Desktop>wglinfo.exe >> OpenGL vendor string: NVIDIA Corporation >> OpenGL renderer string: Quadro 600/PCI/SSE2 >> OpenGL version string: 4.1.0 >> OpenGL extensions (GL_): >> GL_ARB_blend_func_extended, GL_ARB_color_buffer_float, GL_ARB_compatibility, >> >> GL_ARB_copy_buffer, GL_ARB_depth_buffer_float, GL_ARB_depth_clamp, >> GL_ARB_depth_texture, GL_ARB_draw_buffers, GL_ARB_draw_buffers_blend, >> GL_ARB_draw_indirect, GL_ARB_draw_elements_base_vertex, >> GL_ARB_draw_instanced, GL_ARB_ES2_compatibility, >> GL_ARB_explicit_attrib_location, GL_ARB_fragment_coord_conventions, >> GL_ARB_fragment_program, GL_ARB_fragment_program_shadow, >> GL_ARB_fragment_shader, GL_ARB_framebuffer_object, GL_ARB_framebuffer_sRGB, >> GL_ARB_geometry_shader4, GL_ARB_get_program_binary, GL_ARB_gpu_shader5, >> GL_ARB_gpu_shader_fp64, GL_ARB_half_float_pixel, GL_ARB_half_float_vertex, >> GL_ARB_imaging, GL_ARB_instanced_arrays, GL_ARB_map_buffer_range, >> GL_ARB_multisample, GL_ARB_multitexture, GL_ARB_occlusion_query, >> GL_ARB_occlusion_query2, GL_ARB_pixel_buffer_object, >> GL_ARB_point_parameters, GL_ARB_point_sprite, GL_ARB_provoking_vertex, >> GL_ARB_robustness, GL_ARB_sample_shading, GL_ARB_sampler_objects, >> GL_ARB_seamless_cube_map, GL_ARB_separate_shader_objects, >> GL_ARB_shader_bit_encoding, GL_ARB_shader_objects, GL_ARB_shader_precision, >> GL_ARB_shader_subroutine, GL_ARB_shading_language_100, >> GL_ARB_shading_language_include, GL_ARB_shadow, GL_ARB_sync, >> GL_ARB_tessellation_shader, GL_ARB_texture_border_clamp, >> GL_ARB_texture_buffer_object, GL_ARB_texture_buffer_object_rgb32, >> GL_ARB_texture_compression, GL_ARB_texture_compression_bptc, >> GL_ARB_texture_compression_rgtc, GL_ARB_texture_cube_map, >> GL_ARB_texture_cube_map_array, GL_ARB_texture_env_add, >> GL_ARB_texture_env_combine, GL_ARB_texture_env_crossbar, >> GL_ARB_texture_env_dot3, GL_ARB_texture_float, GL_ARB_texture_gather, >> GL_ARB_texture_mirrored_repeat, GL_ARB_texture_multisample, >> GL_ARB_texture_non_power_of_two, GL_ARB_texture_query_lod, >> GL_ARB_texture_rectangle, GL_ARB_texture_rg, GL_ARB_texture_rgb10_a2ui, >> GL_ARB_texture_swizzle, GL_ARB_timer_query, GL_ARB_transform_feedback2, >> GL_ARB_transform_feedback3, GL_ARB_transpose_matrix, >> GL_ARB_uniform_buffer_object, GL_ARB_vertex_array_bgra, >> GL_ARB_vertex_array_object, GL_ARB_vertex_attrib_64bit, >> GL_ARB_vertex_buffer_object, GL_ARB_vertex_program, GL_ARB_vertex_shader, >> GL_ARB_vertex_type_2_10_10_10_rev, GL_ARB_viewport_array, GL_ARB_window_pos, >> >> GL_ATI_draw_buffers, GL_ATI_texture_float, GL_ATI_texture_mirror_once, >> GL_S3_s3tc, GL_EXT_texture_env_add, GL_EXT_abgr, GL_EXT_bgra, >> GL_EXT_bindable_uniform, GL_EXT_blend_color, GL_EXT_blend_equation_separate, >> >> GL_EXT_blend_func_separate, GL_EXT_blend_minmax, GL_EXT_blend_subtract, >> GL_EXT_compiled_vertex_array, GL_EXT_Cg_shader, GL_EXT_depth_bounds_test, >> GL_EXT_direct_state_access, GL_EXT_draw_buffers2, GL_EXT_draw_instanced, >> GL_EXT_draw_range_elements, GL_EXT_fog_coord, GL_EXT_framebuffer_blit, >> GL_EXT_framebuffer_multisample, GL_EXTX_framebuffer_mixed_formats, >> GL_EXT_framebuffer_object, GL_EXT_framebuffer_sRGB, GL_EXT_geometry_shader4, >> >> GL_EXT_gpu_program_parameters, GL_EXT_gpu_shader4, GL_EXT_multi_draw_arrays, >> >> GL_EXT_packed_depth_stencil, GL_EXT_packed_float, GL_EXT_packed_pixels, >> GL_EXT_pixel_buffer_object, GL_EXT_point_parameters, >> GL_EXT_provoking_vertex, GL_EXT_rescale_normal, GL_EXT_secondary_color, >> GL_EXT_separate_shader_objects, GL_EXT_separate_specular_color, >> GL_EXT_shader_image_load_store, GL_EXT_shadow_funcs, >> GL_EXT_stencil_two_side, GL_EXT_stencil_wrap, GL_EXT_texture3D, >> GL_EXT_texture_array, GL_EXT_texture_buffer_object, >> GL_EXT_texture_compression_dxt1, GL_EXT_texture_compression_latc, >> GL_EXT_texture_compression_rgtc, 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_format_BGRA8888, >> GL_EXT_texture_integer, GL_EXT_texture_lod, GL_EXT_texture_lod_bias, >> GL_EXT_texture_mirror_clamp, GL_EXT_texture_object, >> GL_EXT_texture_shared_exponent, GL_EXT_texture_sRGB, GL_EXT_texture_swizzle, >> >> GL_EXT_texture_type_2_10_10_10_REV, GL_EXT_timer_query, >> GL_EXT_transform_feedback2, GL_EXT_vertex_array, GL_EXT_vertex_array_bgra, >> GL_EXT_vertex_attrib_64bit, GL_IBM_rasterpos_clip, >> GL_IBM_texture_mirrored_repeat, GL_KTX_buffer_region, GL_NV_alpha_test, >> GL_NV_blend_minmax, GL_NV_blend_square, GL_NV_complex_primitives, >> GL_NV_conditional_render, GL_NV_copy_depth_to_color, GL_NV_copy_image, >> GL_NV_depth_buffer_float, GL_NV_depth_clamp, GL_NV_explicit_multisample, >> GL_NV_fbo_color_attachments, GL_NV_fence, GL_NV_float_buffer, >> GL_NV_fog_distance, GL_NV_fragdepth, GL_NV_fragment_program, >> GL_NV_fragment_program_option, GL_NV_fragment_program2, >> GL_NV_framebuffer_multisample_coverage, GL_NV_geometry_shader4, >> GL_NV_gpu_program4, GL_NV_gpu_program4_1, GL_NV_gpu_program5, >> GL_NV_gpu_program_fp64, GL_NV_gpu_shader5, GL_NV_half_float, >> GL_NV_light_max_exponent, GL_NV_multisample_coverage, >> GL_NV_multisample_filter_hint, GL_NV_occlusion_query, >> GL_NV_packed_depth_stencil, GL_NV_parameter_buffer_object, >> GL_NV_parameter_buffer_object2, GL_NV_path_rendering, >> GL_NV_pixel_data_range, GL_NV_point_sprite, GL_NV_primitive_restart, >> GL_NV_register_combiners, GL_NV_register_combiners2, >> GL_NV_shader_buffer_load, GL_NV_texgen_reflection, GL_NV_texture_barrier, >> GL_NV_texture_compression_vtc, GL_NV_texture_env_combine4, >> GL_NV_texture_expand_normal, GL_NV_texture_lod_clamp, >> GL_NV_texture_multisample, GL_NV_texture_rectangle, GL_NV_texture_shader, >> GL_NV_texture_shader2, GL_NV_texture_shader3, GL_NV_transform_feedback, >> GL_NV_transform_feedback2, GL_NV_vertex_array_range, >> GL_NV_vertex_array_range2, GL_NV_vertex_attrib_integer_64bit, >> GL_NV_vertex_buffer_unified_memory, GL_NV_vertex_program, >> GL_NV_vertex_program1_1, GL_NV_vertex_program2, >> GL_NV_vertex_program2_option, GL_NV_vertex_program3, >> GL_NVX_conditional_render, GL_NVX_gpu_memory_info, GL_OES_depth24, >> GL_OES_depth32, GL_OES_depth_texture, GL_OES_element_index_uint, >> GL_OES_fbo_render_mipmap, GL_OES_get_program_binary, GL_OES_mapbuffer, >> GL_OES_packed_depth_stencil, GL_OES_rgb8_rgba8, GL_OES_standard_derivatives, >> >> GL_OES_texture_3D, GL_OES_texture_float, GL_OES_texture_float_linear, >> GL_OES_texture_half_float, GL_OES_texture_half_float_linear, >> GL_OES_texture_npot, GL_OES_vertex_array_object, GL_OES_vertex_half_float, >> GL_SGIS_generate_mipmap, GL_SGIS_texture_lod, GL_SGIX_depth_texture, >> GL_SGIX_shadow, GL_SUN_slice_accum, GL_WIN_swap_hint, WGL_EXT_swap_control. >> >> WGL extensions: >> WGL_ARB_buffer_region, WGL_ARB_create_context, >> WGL_ARB_create_context_profile, WGL_ARB_create_context_robustness, >> WGL_ARB_extensions_string, WGL_ARB_make_current_read, WGL_ARB_multisample, >> WGL_ARB_pbuffer, WGL_ARB_pixel_format, WGL_ARB_pixel_format_float, >> WGL_ARB_render_texture, WGL_ATI_pixel_format_float, >> WGL_EXT_create_context_es2_profile, WGL_EXT_extensions_string, >> WGL_EXT_framebuffer_sRGB, WGL_EXT_pixel_format_packed_float, >> WGL_EXT_swap_control, WGL_NVX_DX_interop, WGL_NV_DX_interop, >> WGL_NV_DX_interop2, WGL_NV_copy_image, WGL_NV_float_buffer, >> WGL_NV_gpu_affinity, WGL_NV_multisample_coverage, >> WGL_NV_render_depth_texture, WGL_NV_render_texture_rectangle, >> WGL_NV_swap_group, WGL_NV_video_capture. >> >> visual x bf lv rg d st ge ge r g b a ax dp st accum buffs ms >> id dep cl sp sz l ci b ro ne ac sz sz sz sz bf th cl r g b a ns b >> ----------------------------------------------------------------------- >> 0x01 32 wn . 32 . r . . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0x02 32 wn . 32 . r . . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0x03 32 wn . 32 . r . . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0x04 32 wn . 32 . r . . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0x05 32 wn . 32 . r . . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x06 32 wn . 32 . r . . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0x07 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0x08 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0x09 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0x0a 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0x0b 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x0c 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0x0d 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0x0e 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0x0f 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0x10 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0x11 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x12 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0xf5 32 wn . 32 . r . . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0xf6 32 wn . 32 . r . . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0xf7 32 wn . 32 . r . . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0xf8 32 wn . 32 . r . . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0xf9 32 wn . 32 . r . . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0xfa 32 wn . 32 . r . . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0xfb 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0xfc 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0xfd 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0xfe 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0xff 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x100 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0x101 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0x102 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0x103 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0x104 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0x105 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x106 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0x16f 32 wn . 32 . r . . y . 8 8 8 . . 32 8 16 16 16 . 0 0 >> 0x170 32 wn . 32 . r . . y . 8 8 8 . . 16 8 16 16 16 . 0 0 >> 0x171 32 wn . 32 . r y . y . 8 8 8 . . 32 8 16 16 16 . 0 0 >> 0x172 32 wn . 32 . r y . y . 8 8 8 . . 16 8 16 16 16 . 0 0 >> 0x173 32 wn . 32 . r . . y . 8 8 8 8 . 32 8 16 16 16 16 0 0 >> 0x174 32 wn . 32 . r . . y . 8 8 8 8 . 16 8 16 16 16 16 0 0 >> 0x175 32 wn . 32 . r y . y . 8 8 8 8 . 32 8 16 16 16 16 0 0 >> 0x176 32 wn . 32 . r y . y . 8 8 8 8 . 16 8 16 16 16 16 0 0 >> 0x177 32 wn . 32 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x178 32 wn . 32 . c . . y . . . . . . 16 8 . . . . 0 0 >> 0x179 32 wn . 32 . c y . y . . . . . . 32 8 . . . . 0 0 >> 0x17a 32 wn . 32 . c y . y . . . . . . 16 8 . . . . 0 0 >> 0x17b 24 bm . 24 . r . . y . 8 8 8 . . 32 8 16 16 16 . 0 0 >> 0x17c 24 bm . 24 . r . . y . 8 8 8 . . 16 8 16 16 16 . 0 0 >> 0x17d 24 bm . 24 . r . . y . 8 8 8 8 . 32 8 16 16 16 16 0 0 >> 0x17e 24 bm . 24 . r . . y . 8 8 8 8 . 16 8 16 16 16 16 0 0 >> 0x17f 24 bm . 24 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x180 24 bm . 24 . c . . y . . . . . . 16 8 . . . . 0 0 >> 0x181 16 bm . 16 . r . . y . 5 5 5 . . 32 8 11 11 10 . 0 0 >> 0x182 16 bm . 16 . r . . y . 5 5 5 . . 16 8 11 11 10 . 0 0 >> 0x183 16 bm . 16 . r . . y . 5 5 5 8 . 32 8 8 8 8 8 0 0 >> 0x184 16 bm . 16 . r . . y . 5 5 5 8 . 16 8 8 8 8 8 0 0 >> 0x185 16 bm . 16 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x186 16 bm . 16 . c . . y . . . . . . 16 8 . . . . 0 0 >> 0x187 8 bm . 8 . r . . y . 3 3 2 . . 32 8 11 11 10 . 0 0 >> 0x188 8 bm . 8 . r . . y . 3 3 2 . . 16 8 11 11 10 . 0 0 >> 0x189 8 bm . 8 . r . . y . 3 3 2 8 . 32 8 8 8 8 8 0 0 >> 0x18a 8 bm . 8 . r . . y . 3 3 2 8 . 16 8 8 8 8 8 0 0 >> 0x18b 8 bm . 8 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x18c 8 bm . 8 . c . . y . . . . . . 16 8 . . . . 0 0 >> 0x18d 4 bm . 4 . r . . y . 1 1 1 . . 32 8 5 6 5 . 0 0 >> 0x18e 4 bm . 4 . r . . y . 1 1 1 . . 16 8 5 6 5 . 0 0 >> 0x18f 4 bm . 4 . r . . y . 1 1 1 8 . 32 8 4 4 4 4 0 0 >> 0x190 4 bm . 4 . r . . y . 1 1 1 8 . 16 8 4 4 4 4 0 0 >> 0x191 4 bm . 4 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x192 4 bm . 4 . c . . y . . . . . . 16 8 . . . . 0 0 >> ----------------------------------------------------------------------- >> visual x bf lv rg d st ge ge r g b a ax dp st accum buffs ms >> id dep cl sp sz l ci b ro ne ac sz sz sz sz bf th cl r g b a ns b >> ----------------------------------------------------------------------- >> ########## >> >> >> >> >> >> On 6/27/11 4:42 PM, Greg Couch wrote: >>> Those settings should work for Chimera too. Please download >>> http://www.cgl.ucsf.edu/home/gregc/wglinfo.exe, run it in a terminal window >>> (eg., All Programs / Accessories / Command Prompt), and send the results >>> directly back to me. wglinfo lists all of the possible OpenGL framebuffer >>> configurations and should confirm if OpenGL is reporting that stereo is >>> available and with which graphics capabilities. I'll summarize what I find >>> to chimera-users. >>> >>> -- Greg >>> >>> On 06/27/2011 12:34 PM, William Joseph Allen wrote: >>>> Hi Greg, >>>> >>>> Thank you very much for your quick reply. >>>> >>>> I had actually already changed those settings in the Nvidia control panel. >>>> They are as follows: >>>> >>>> Stereo - Enable: 'On' >>>> Stereo - Display mode: 'Generic active stereo (with NVIDIA 3D vision)' >>>> >>>> The display mode you mentioned in your reply was not an option in my Nvidia >>>> control panel. Although, this is the only setting that really makes sense >>>> for what I am doing, and I tried most of the other settings without >>>> success. I also tried toggling some of the other features in a non-random >>>> way, but without success. >>>> >>>> These two settings, however, are the changes that made stereo in VMD and >>>> MOE start working (both of which use OpenGL). But, for whatever reason, >>>> Chimera still gives those previously mentioned errors when I try to turn on >>>> stereo. If it helps, the monitor is an Asus 120 Hz LCD display connected by >>>> a dual-link DVI cable directly to the graphics card. No DIN connector is >>>> involved. >>>> >>>> Thanks again, >>>> >>>> William Allen >>>> >>>> >>>> >>>> On 6/27/11 1:42 PM, Greg Couch wrote: >>>>> It's should be a driver configuration issue. There are two different 3D >>>>> graphics APIs on Windows, Direct3D and OpenGL, and most Windows >>>>> applications use the former and Chimera uses the latter (because it works >>>>> on Linux and Mac OS X too). To configure OpenGL stereo in the Quadro >>>>> driver on Windows, bring up the NVIDIA Control Panel, navigate to 3D >>>>> Settings, then Manage 3D Settings. And in those options, set "Stereo - >>>>> Enable" to on, and "Stereo - Display mode" to the appropriate type of >>>>> stereo, in your case, my guess would be "On-board DIN connector (with >>>>> NVIDIA 3D Vision)". >>>>> >>>>> HTH, >>>>> >>>>> Greg >>>>> >>>>> On 06/27/2011 08:02 AM, William Joseph Allen wrote: >>>>>> Hello Chimera Users, >>>>>> >>>>>> I am trying to view molecules in sequential stereo in Chimera (v 1.5.3). >>>>>> When I >>>>>> choose Camera -> Sequential Stereo, I get an error that says: "Unable to >>>>>> turn on >>>>>> stereo viewing (Unable to find hardware support / couldn't choose pixel >>>>>> format / >>>>>> Couldn't configure tool widget)". >>>>>> >>>>>> Here is a little bit of the background: >>>>>> >>>>>> The machine is a new Dell desktop running 64-bit Windows 7. I installed a >>>>>> Quadro >>>>>> 600 graphic cards, and I am using the Nvidia 3D vision wireless glasses >>>>>> kit. The >>>>>> version of the Nvidia driver is 275.36, which I believe is the latest >>>>>> version. I >>>>>> should also note that I was able to successfully configure VMD and MOE to >>>>>> work >>>>>> in Stereo with set up described, so I know that 3D should work, I just >>>>>> can't get >>>>>> it to work in Chimera. >>>>>> >>>>>> Previous messages in the mailing archive seem to indicate that the >>>>>> specific type >>>>>> of graphics card or the version of the driver is usually the problem. >>>>>> From what >>>>>> I have read, the Quadro 600 should be compatible. I guess my only concern >>>>>> is the >>>>>> version of the driver. It seems there was some bugs in the 197.x, 258.x, and >>>>>> 259.x versions of the driver, and 266.45 was reported to work. I have >>>>>> version >>>>>> 275.36, should I be worried about a bug or is there something else I missed? >>>>>> >>>>>> Than you for your help, >>>>>> >>>>>> William Allen >>>> >>>> >>> >>> >> > > -- William Joseph Allen, Ph.D. Robert C. Rizzo Research Group Department of Applied Mathematics and Statistics Stony Brook University http://rizzo.ams.sunysb.edu/~wjallen/

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creating a peptide bond between two fragments
by Glenn Millhauser 28 Jun '11

28 Jun '11

Hi Folks, I am trying to add a four amino acid segment to the N-terminus of a protein in the pdb. I can generate the four residue stretch and move its C-term close to the N-term of the structured protein. I can then select the C' and N atoms, which are about 1.0 Angstrom apart. At that point, I am stuck. Not sure how to add a bond and then create a proper structure. I've played around with Join Models, but no luck. Without a peptide bond recognized by Chimera, ribbons are discontinuous. Any ideas? Many thanks, glenn Glenn L. Millhauser Department of Chemistry & Biochemistry UC Santa Cruz Santa Cruz, CA 95064 831 459 2176 voice 831 566 3337 cell 831 459 2935 fax 831 824 4645 google voice glennm(a)ucsc.edu http://chemistry.ucsc.edu/~glennm http://www.chemistry.ucsc.edu/faculty/millhauser.html

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Capping a clipped sphere representation
by Michelle E. McCully 28 Jun '11

28 Jun '11

Hi, I would like to create an image of a protein shown in van der Waals spheres with a clipped surface. I'd like each individual sphere/atom to be capped and colored the same color as the atom. Is this possible? I can show the protein in spheres and clip it using the side view dialog, but the clipped spheres show up as shells instead of solid balls. I also have found directions for capping and coloring surfaces, but I don't see a way to make the clipped surface colored by atom. It seems that building my protein out of sphere shapes and clipping that would give me the desired effect, but I was hoping there was something easier and built-in that I'm missing. Thanks for your help, Michelle

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Stable 64bit version
by Guy Hughes 28 Jun '11

28 Jun '11

Hello, I am an MPhil researcher at the University of Manchester based in laboratory of Professor Bob Ford. I have been using cryo-electron tomography to build a 3D volume containing mucins (High Mr heavily glycosylated polypeptides) which are what my research focusses on. We use a Tecnai 300kV Polara and Gatan's Digital Micrograph software to create tomograms of our samples and then IMOD to view them. Recently I was told that Chimera would be a very useful tool when married with the data from IMOD so I downloaded a copy from your website. I regret to admit that I had several problems with the programme and eventually had to delete. The main problem was that my computer continued to blue-screen and perform very slowly if at all. The labtop I was using has the following spec.; CPU: Intel Core i5 VGA: NVIDIA Geforce 310M/1GB DDR3 RAM: DDRIII 4GB (2GB*2) OS: Windows 7 64-bit Is my PC inadequate or is it possible I downloades a corrupted/unstable version of Chimera? I would very much like to try and start using Chimera again but would first like some advice on what the original problem may have been. Any suggestions or help would be greatly appreciated. Thanks, Guy Hughes.

2 1

chimera setup
by yp sun 28 Jun '11

28 Jun '11

Dear sir, I want to setup the chimera 1.5.3 program on windows XP system, but the setup cannot be finished, it retures a error information that says: "Unable to excute file: C:/program file/chimera 1.5.3/bin/pythonn.exe." How can I solve the problem? Thanks. Best regards Yeping Sun PhD CAS Key Laboratory of Pathogenic Microbiology & Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

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Chimera-users June 2011