- Chimera-users - RBVI Mailing Lists

Tear-off menus in Chimera 1.5.3 for Mac OS X
by Jeff Lawton 11 Jul '11

11 Jul '11

Hi, I am running the native aqua version of Chimera 1.5.3 on Mac OS X 10.6, and it seems that the "tear off" feature of the menus is not available, though I was previously able to do that when running the X window version of Chimera. Is there a way to use the menu "tear off" feature in the native aqua version? Thanks! Jeff -- Associate Professor of Biochemistry Department of Chemistry Eastern University 1300 Eagle Road St. Davids, PA 19087 (610) 341-1545

3 2

Re: [Chimera-users] distance between 2 residues
by Dedan Githae 11 Jul '11

11 Jul '11

how is the problem solved in chimera? i want to measure distance between 2 residues

2 2

Invitation à se connecter sur LinkedIn
by Vincent Zoete 07 Jul '11

07 Jul '11

LinkedIn ------------ J'aimerais vous inviter à rejoindre mon réseau professionnel en ligne, sur le site LinkedIn. Vincent Vincent Zoete Associate group leader chez Swiss Institute of Bioinformatics Région de Genève, Suisse Veuillez confirmer que vous connaissez Vincent Zoete https://www.linkedin.com/e/vxh6i1-gpupen7z-1e/isd/3469346511/KWdfhuHl/ -- (c) 2011, LinkedIn Corporation

1 0

Problem with multiple monitors and NVidia 3D Vision - any suggestions ?
by Steven Ludtke 07 Jul '11

07 Jul '11

Hi. I just set up a 3-D vision compatible stereo monitor as a second display on my desktop. I have a Quadro 4000 video card and am running 64 bit linux (Ubuntu 11.04) with the latest 270.41.06 Nvidia driver. If I only have one monitor (the stereo capable one) attached to the machine, I can get stereo working (looks very nice), but if I have the second non-stereo capable monitor connected at the same time, it will not initialize the stereo display mode (on either display). I have it configured using Xinerama, so the 2 displays are on separate X-servers. Even when I disable Xinerama, and the second display is running on a completely independent Screen, it still won't go into stereo mode. Here are the relevant lines from the Xorg log file: [ 9016.284] (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 [ 9016.284] (==) NVIDIA(0): RGB weight 888 [ 9016.284] (==) NVIDIA(0): Default visual is TrueColor [ 9016.284] (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) [ 9016.285] (**) NVIDIA(0): Option "TwinView" "0" [ 9016.285] (**) NVIDIA(0): Option "MetaModes" "nvidia-auto-select +0+0" [ 9016.285] (**) NVIDIA(0): Option "TwinViewXineramaInfoOrder" "DFP-2" [ 9018.424] (II) NVIDIA(GPU-0): Display (DELL3007WFPHC (DFP-0)) does not support NVIDIA 3D [ 9018.424] (II) NVIDIA(GPU-0): Vision stereo. [ 9018.466] (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 [ 9018.466] (==) NVIDIA(1): RGB weight 888 [ 9018.466] (==) NVIDIA(1): Default visual is TrueColor [ 9018.466] (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) [ 9018.467] (**) NVIDIA(1): Option "Stereo" "10" [ 9018.467] (**) NVIDIA(1): Option "TwinView" "0" [ 9018.467] (**) NVIDIA(1): Option "MetaModes" "1920x1080_120 +0+0" [ 9018.467] (**) NVIDIA(1): USB IR emitter stereo requested [ 9019.116] (II) NVIDIA(GPU-1): Display (Acer HN274H (DFP-0)) supports NVIDIA 3D Vision [ 9019.116] (II) NVIDIA(GPU-1): stereo. [ 9019.117] (II) NVIDIA(1): NVIDIA GPU Quadro 4000 (GF100GL) at PCI:2:0:0 (GPU-1) [ 9019.117] (--) NVIDIA(1): Memory: 2097152 kBytes [ 9019.117] (--) NVIDIA(1): VideoBIOS: 70.00.37.00.03 [ 9021.570] (II) NVIDIA(1): USB emitter - Copyright (c) 2009 NVIDIA Corporation NVIDIA [ 9021.570] (II) NVIDIA(1): stereo controller [ 9021.598] (II) NVIDIA(1): Setting mode "1920x1080_120+0+0" So, the logfile seems to indicate that it's initialized correctly, but when chimera tries to open a Stereo window, it raises an error :^( Here are the relevant xorg.conf sections: Section "ServerLayout" Identifier "Layout0" Screen 0 "Screen0" 0 0 Screen 1 "Screen1" 2560 0 InputDevice "Keyboard0" "CoreKeyboard" InputDevice "Mouse0" "CorePointer" Option "Xinerama" "1" Option "XineramaStereoFlipping" "0" EndSection Section "Device" Identifier "Device0" Driver "nvidia" VendorName "NVIDIA Corporation" BoardName "Tesla C2070" BusID "PCI:131:0:0" EndSection Section "Device" Identifier "Device1" Driver "nvidia" VendorName "NVIDIA Corporation" BoardName "Quadro 4000" BusID "PCI:2:0:0" EndSection Section "Screen" Identifier "Screen0" Device "Device0" Monitor "Monitor0" DefaultDepth 24 Option "TwinViewXineramaInfoOrder" "DFP-2" Option "TwinView" "0" Option "metamodes" "nvidia-auto-select +0+0" SubSection "Display" Depth 24 EndSubSection EndSection Section "Screen" # Removed Option "metamodes" "nvidia-auto-select +0+0" Identifier "Screen1" Device "Device1" Monitor "Monitor1" DefaultDepth 24 Option "TwinView" "0" Option "metamodes" "1920x1080_120 +0+0" Option "Stereo" "10" SubSection "Display" Depth 24 EndSubSection EndSection Section "Extensions" Option "Composite" "Disable" EndSection Anyone else have a Stereo configuration with dual monitors working ? cheers ---------------------------------------------------------------------------- Steven Ludtke, Ph.D. Associate Professor Co-Director National Center For Macromolecular Imaging Dept of Biochemistry and Mol. Biol. Baylor College of Medicine sludtke(a)bcm.edu stevel(a)alumni.caltech.edu

2 4

Re: [Chimera-users] Regarding adding plane surfaces....
by Elaine Meng 07 Jul '11

07 Jul '11

On Jul 6, 2011, at 11:23 PM, chinmaya joshi wrote: > Hi Elaine, > > I have three objects in the chimera image. > All these objects are in different planes. > How to add surfaces to each of these so that they can be shown to lie in diff planes? > I have attached a typical image herewith. > > Regards, > Chinmaya Hi Chinmaya, There is a tool to define planes from sets of atoms, but I don't know if you have atoms. The "objects" (your image included below) look like isosurfaces in one volume data set. If you had atoms to start with, for example if you made the volume from atoms using the command "molmap", you could go back to those atoms use them to define planes. It could be done with the "define" command or "Axes/Planes/Centroids" (under Tools... Structure Analysis). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru…> I don't know any way to define planes for isosurface blobs directly, without atoms. However, if you can calculate the plane coordinates yourself from these blobs, you can create plane objects with those coordinates in the BILD format. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> The last idea is that you can use the Volume Viewer tool, Features menu entry "Planes" to view only certain slices of your data at a time, but this does not draw a plane object. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum…> Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of directly to me. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Chimera function
by Flora Ieong 07 Jul '11

07 Jul '11

To whom it may concern, I am a chimera user and am currently doing a glycan research using Chimera 1.5.3. I wonder if chimera has a function to add glycans to a protein. Thank You. Sincerely, Pek Ieong

2 2

movie script
by Jean-Francois Menetret 06 Jul '11

06 Jul '11

Hello, I am trying to make a movie to illustrate a conformational change between two PDBs; I would like to turn the objects while switching from one to the other. Could you give me some pointers ? Thank you J-F

2 1

Re: [Chimera-users] Drug-Metal Complexation Modeling
by Mickey Branham 06 Jul '11

06 Jul '11

Thanks Elaine, I did check out the CCL website; a great resource. Mickey >>> Elaine Meng 07/05/11 6:25 PM >>> Hi Mickey, I don't have experience in this area, but you might try asking on the Computational Chemistry List (www.ccl.net) as to what programs might be suitable for predicting the structure of your complex. One way is to use their web form http://www.ccl.net/cgi-bin/ccl/send_ccl_message Best, 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 Jul 2, 2011, at 1:46 AM, Mickey Branham wrote: > 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 Please find our Email Disclaimer here: http://www.ukzn.ac.za/disclaimer/

1 0

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] 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/

2 1

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

2 1

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

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/

2 1

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

4 6

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.

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

2 1

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

3 2

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

2 2

Stereo vision with Quadro 600
by William Joseph Allen 27 Jun '11

27 Jun '11

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

2 3

Select
by George Tzotzos 27 Jun '11

27 Jun '11

Can anyone provide some help. I'm trying to select two specific oxygen atoms in different residues (98 and 142). The command select :142@O1 :98@O1 selects only 1 atom (that of residue 142). I tried select :98@O1 only. The output is "selection" cleared. I'm rather puzzled. Any help would be greatly appreciated Regards George

2 1

pdb to xml
by Damien LARIVIERE 24 Jun '11

24 Jun '11

Dear all, WritePDB enables to save a displayed structure in the pdb format. Is there a way to save the structure into the PDBML format? If not, do you know a (simple) way to do that? Many thanks Damien

2 1

Water Ice Structures
by Matthew Thompson 24 Jun '11

24 Jun '11

I am looking for the crystal structures of "normal" ice (Ih), ice(VI), and ice(VII). I have found the .cif file for ice(VI), but I can't seem to get it to load properly into Chimera. I am really only familiar with using pdb's in Chimera. These would be used in a presentation given this coming weekend at the National School for Neutron and X-ray Scattering. Any help in this would be greatly appreciated Thanks Matt _ Matthew K. Thompson, PhD North Carolina State University Raleigh, NC 27695 Office: 919-515-2105 Cell: 919-455-1775

4 7

Re: [Chimera-users] Drug-Metal Complexation Modeling
by Elaine Meng 23 Jun '11

23 Jun '11

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. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/metalgeom/metalgeo…> 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. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht…> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.…> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.…> 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 >

1 0

computer advice
by Ryan Woltz 21 Jun '11

21 Jun '11

Dear Chimera, We are looking at getting a new computer for our lab to used for only modeling. We are planning using chimera, pymol, and dock 6.4 as primary programs for this. What specifications i.e. graphic cards, ram, do you recommend us getting? Thank you, Ryan Woltz UC Davis Cardiology

2 1