- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Drug-Metal Complexation Modeling
by Mickey Branham 05 Jul '11

05 Jul '11

Thanks Elaine, Yes, your comments were helpful. I did a bit of window shopping with Chimera (very impressive) but I think for this project it may not be the right set of tools. Briefly, what we're trying to do is to produce stable complexes of the dipeptide carnosine with a heavy metal (i.e. ruthenium III) by high energy ball milling. So far this approach has been effective in producing nanosized particles which do contain [carn-Ru] complexes (ca. XRD, DSC/TGA, and FTIR) but their structure and molecularity appear to be polydispersed. We are trying to predict the most stable complex stoichiometry so that we can optimize milling parameters (e.g. temp, inert gas, speed and time) known to influence complex formation rate. Once we are able to reproducibly form the [carn-Ru] complex our plan is to characterize its anti-viral or anti-tumor activty. Don't know if this seems interesting but any comments from you would be appreciated. Thanks again for your response. Cheers Mickey >>> Elaine Meng 06/23/11 6:23 PM >>> Hello Mickey, Chimera has a "Metal Geometry" tool for assessing the coordination geometry within metal complexes, for example, identifying a protein complexation site as octahedral vs. pentagonal bipyramidal. It is intended for use with existing coordinates, such as from crystallography or output by other computational methods. Chimera does not include QM calculations, and would not replace the programs you mention if you are primarily interested in generating the coordinates in the first place. You can build structures with Chimera, but optimization is rather limited to only a few metals, and those that are handled are treated as point-charge VDW spheres (only minimization, no MD, and no QM to incorporate orbital directionality). It could be useful modifying existing metal complex structures, and as mentioned above, analyzing those structures output from other programs. 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 Jun 22, 2011, at 11:11 PM, Mickey Branham wrote: > Dr. Meng > Our group is interested in drug-metal complexation modeling. We have ongoing MM and MD studies using Gaussian or COSMO, with mixed results. Before we embark on a new voyage into Chimera can you tell us its capacity for elucidating drug-metal complexes e.g. tetracycline-M+2. > > Cheers > Mickey > > Michael Lee Branham, PhD. > University of KwaZulu-Natal > School of Pharmacy and Pharmacology > Durban, South Africa > > Please find our Email Disclaimer here-->: http://www.ukzn.ac.za/disclaimer > Please find our Email Disclaimer here: http://www.ukzn.ac.za/disclaimer/

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System requirements
by יוכבד 04 Jul '11

04 Jul '11

Hi I'm looking into upgrading my computer and I was wondering whether Chimera runs properly on Windows7 and with a NVIDIA GT430 1GB graphic card. Thank you Yocheved

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Coordinates
by George Tzotzos 01 Jul '11

01 Jul '11

Hi everybody, Is there a way to find out the coordinates of the centre of mass of (a) protein; (b) a specific residue in a protein; (c) a ligand bound on a protein. I searched the Chimera documentation but didn't find anything appropriate. Maybe that my search terms were wrong. Many thanks and best regards George

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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

4 5

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.

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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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preserving the serial numbering
by George White 28 Jun '11

28 Jun '11

Hi, I am wondering is there any way to write a pdb from Chimera that preserves the original atom serial numbering of the input pdb. Chimera seems to apply its own renumbering (i.e. making the number of the 1st atom #1 etc.) . Thanks in advance, George

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ViewDock compound state
by S. Pea 27 Jun '11

27 Jun '11

Hello, I was wondering if there is an option in ViewDock to create more bins (flags) in the "change compound state"? Currently there is an option to change the compound state from Viable, to either Deleted or Purged but is there an option to put extra user defined states. Thanks, Magdalena

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