March 2015 - Chimera-users - RBVI Mailing Lists

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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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

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layering problem
by Joseph Atherton 20 Aug '15

20 Aug '15

Hi! I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this? Cheers, Joe

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scale bar
by Dmitry 27 May '15

27 May '15

Dear developers, How are you? I have a question about scale bar. I am not completely sure that the scale bar I drew is correct. What are the scale settings for drawing the scale bar? By the default the scale bar is in Angstroms isn’t it? In ImageJ there is a possibility to set the scale 1 pixel = X value (nm/Å/etc) Is there the same possibility in Chimera? Thank you Sincerely, Dmitry

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segname
by Francesco Pietra 04 Apr '15

04 Apr '15

Hello: May I ask whether there is till a problem in having CHIMERA understanding segname? For those working with XPLOR (NAMD, for example) and multichain proteins, rendering results with CHIMERA becomes very tedious (having to use atom indexes) Thanks francesco pietra

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New molecule from selection?
by Oliver Clarke 03 Apr '15

03 Apr '15

Hi, This may already be implemented, but I couldn’t find it - the nearest equivalent feature I know of is copy/combine, but that only works on whole models, not taking into account selections. I was wondering if it would be possible to implement a feature creating a new model comprised of all atoms in the current selection? This would be particularly helpful when combining many parts of multiple models, or when creating a separate model consisting of a subselection of the current model. This can be done at present using a combination of copy/combine and selecting and deleting those parts of the copied molecules that are not in the selection, but this gets messy for complicated selections. Best, Oliver.

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Request for axes measurements
by Jayaraman T 31 Mar '15

31 Mar '15

Hi, I'm Jayaraman, pursuing PhD in Protein Engineering at Pusan National University. I just want to calculate the Axes for specific set of helical residue CA atoms and then to calculate the angle between them. Is it possible with Chimera and if so, please do help me out that how to do it. It would be grateful and looking forward to hear at your earliest convenience. Thank you. - - With warm regards Jram | 201493155 PhD Scholar jram(a)pusan.ac.kr Bio molecular Engineering Lab Dept of Chemical Engineering Pusan National University Busan, South Korea +8210 9906 3680

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Picking not working in RDS
by Hurt, Darrell (NIH/NIAID) [E] 31 Mar '15

31 Mar '15

Hi Chimera friends, I'm using the Microsoft Remote Desktop Mac client to connect to a Microsoft Remote Desktop Server (an "RDS" running Windows Server 2012 R2). That RDS is serving out a Windows 8 environment and I'm running the latest Chimera release in it very successfully. Except that selection by picking (Ctrl-mouse_button_1) and centering (Ctrl-mouse_button_3) does NOT work. When I try to select by picking, the cursor changes from the arrow to hand momentarily. I also get this behavior when connecting to the RDS via any other client. Any thoughts on what might be happening and how to fix it? Thanks, Darrell -- Darrell Hurt, Ph.D. Acting Chief Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 5601 Fishers Lane, 4A31 North Bethesda, MD 20852 Office: 240-669-2741 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> , @NIH3Dprint<https://twitter.com/nih3dprint> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Toggle active vs displayed for checkboxes at bottom of screen?
by Oliver Clarke 30 Mar '15

30 Mar '15

Hi, this is more of a feature suggestion than anything, and I guess it is unlikely to be implemented before Chimera 2, but thought I’d put it out there anyway. Currently the checkboxes at the bottom of the main display control whether or not a model is active - this is very handy when reorienting models with respect to one another. I would love a similar means to toggle the display of individual models without going to the model panel. One way would be to alter the “Active models” text label (circled in screenshot) to “Displayed models”, and change the behaviour/meaning of the checkboxes accordingly, similar to the A/I/R/S selection mode changer at the bottom right of the main display. So you would click “Active models”, and the text would switch to “Displayed models”, and the configuration of the checkboxes would change so that the displayed models (rather than the active models) are checked. Is this something that would be possible in a future version? Best, Oliver.

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Re: [Chimera-users] Running graphical Chimera from remote server
by Hurt, Darrell (NIH/NIAID) [E] 30 Mar '15

30 Mar '15

Hello again, I still have to try VirtualGL (as suggested on a previous thread). However, I want to share the following information: I learned that the 60 fps I was getting on glxgears is likely due to Ubuntu having "sync" enabled by default, which means that glxgears always runs at about 60 fps. So let's ignore that bit of information. http://askubuntu.com/questions/31488/how-to-test-if-my-video-card-has-3d-su pport My glxinfo (see below at "OpenGL renderer string") suggests that I have an NVIDIA graphics card installed. But "lspci -vnn | grep -i VGA" suggests that I have a simple Matrox graphics card: <output of lspci> 01:00.1 VGA compatible controller [0300]: Matrox Electronics Systems Ltd. MGA G200EH [102b:0533] (rev 01) (prog-if 00 [VGA controller]) <output of glxinfo> name of display: localhost:11.0 display: localhost:11 screen: 0 direct rendering: No (If you want to find out why, try setting LIBGL_DEBUG=verbose) server glx vendor string: SGI server glx version string: 1.4 server glx extensions: GLX_ARB_create_context, GLX_ARB_create_context_profile, GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_OML_swap_method, GLX_SGIS_multisample, GLX_SGIX_fbconfig client glx vendor string: Mesa Project and SGI client glx version string: 1.4 client glx extensions: GLX_ARB_create_context, GLX_ARB_create_context_profile, GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_EXT_framebuffer_sRGB, GLX_EXT_create_context_es2_profile, GLX_MESA_copy_sub_buffer, GLX_MESA_multithread_makecurrent, GLX_MESA_swap_control, GLX_OML_swap_method, GLX_OML_sync_control, GLX_SGI_make_current_read, GLX_SGI_swap_control, GLX_SGI_video_sync, GLX_SGIS_multisample, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_SGIX_visual_select_group, GLX_EXT_texture_from_pixmap, GLX_INTEL_swap_event GLX version: 1.4 GLX extensions: GLX_ARB_create_context, GLX_ARB_create_context_profile, GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_MESA_multithread_makecurrent, GLX_OML_swap_method, GLX_SGI_make_current_read, GLX_SGIS_multisample, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: NVIDIA GeForce 9400M OpenGL Engine OpenGL version string: 1.4 (2.1 NVIDIA-8.16.81 310.40.00.20f04) OpenGL extensions: GL_ARB_depth_texture, GL_ARB_draw_buffers, GL_ARB_fragment_program, GL_ARB_fragment_program_shadow, GL_ARB_imaging, GL_ARB_multisample, GL_ARB_multitexture, GL_ARB_occlusion_query, GL_ARB_point_parameters, GL_ARB_point_sprite, GL_ARB_shadow, GL_ARB_texture_border_clamp, GL_ARB_texture_compression, GL_ARB_texture_cube_map, GL_ARB_texture_env_add, GL_ARB_texture_env_combine, GL_ARB_texture_env_crossbar, GL_ARB_texture_env_dot3, GL_ARB_texture_mirrored_repeat, GL_ARB_texture_non_power_of_two, GL_ARB_texture_rectangle, GL_ARB_transpose_matrix, GL_ARB_vertex_program, GL_ARB_window_pos, GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color, GL_EXT_blend_equation_separate, GL_EXT_blend_func_separate, GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_clip_volume_hint, GL_EXT_draw_range_elements, GL_EXT_fog_coord, GL_EXT_framebuffer_object, GL_EXT_multi_draw_arrays, GL_EXT_point_parameters, GL_EXT_rescale_normal, GL_EXT_secondary_color, GL_EXT_separate_specular_color, GL_EXT_shadow_funcs, GL_EXT_stencil_two_side, GL_EXT_stencil_wrap, GL_EXT_texture_compression_dxt1, GL_EXT_texture_compression_s3tc, GL_EXT_texture_edge_clamp, GL_EXT_texture_env_add, GL_EXT_texture_filter_anisotropic, GL_EXT_texture_lod_bias, GL_EXT_texture_mirror_clamp, GL_EXT_texture_rectangle, GL_APPLE_packed_pixels, GL_ATI_draw_buffers, GL_ATI_texture_env_combine3, GL_ATI_texture_mirror_once, GL_ATIX_texture_env_combine3, GL_IBM_texture_mirrored_repeat, GL_INGR_blend_func_separate, GL_NV_blend_square, GL_NV_depth_clamp, GL_NV_fog_distance, GL_NV_fragment_program_option, GL_NV_fragment_program2, GL_NV_light_max_exponent, GL_NV_multisample_filter_hint, GL_NV_point_sprite, GL_NV_texgen_reflection, GL_NV_texture_rectangle, GL_NV_vertex_program2_option, GL_NV_vertex_program3, GL_SGIS_generate_mipmap, GL_SGIS_texture_border_clamp, GL_SGIS_texture_edge_clamp, GL_SGIS_texture_lod, GL_SUN_multi_draw_arrays -- Darrell Hurt, Ph.D. Acting Chief Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 5601 Fishers Lane, 4A31 North Bethesda, MD 20852 Office: 240-669-2741 Mobile: 301-758-3559Web: BCBB Home Page <http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb .aspx#niaid_inlineNav_Anchor> Twitter: @niaidbioit <https://twitter.com/niaidbioit> , @NIH3Dprint <https://twitter.com/nih3dprint> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. On 3/29/15 7:10 PM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh(a)niaid.nih.gov> wrote: >Hi Chimera friends, > >I want to run a graphics-enabled Chimera from a remote Ubuntu server. The >Ubuntu server is quite beefy (and not virtualized), but it has a stock >video card. When I run "glxgears", I can see the gears and get about 60 >fps (reported), but the gears don't move and aren't interactive. > >I found this message from the listserv a few years ago that recommends >the use of VirtualGL: >http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007953.ht >ml > >My X windowing system is Xquartz on a Mac. Is my problem related to >software GL or to the poor graphics card? > >Related question: what X windowing system do you recommend on a Windows >system? CYGWIN? > >Thanks, >Darrell > >-- >Darrell Hurt, Ph.D. >Acting Chief >Bioinformatics and Computational Biosciences Branch (BCBB) >OCICB/OSMO/OD/NIAID/NIH > >5601 Fishers Lane, 4A31 >North Bethesda, MD 20852 >Office: 240-669-2741 >Mobile: 301-758-3559 >Web: BCBB Home >Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages >/bcbb.aspx#niaid_inlineNav_Anchor> >Twitter: @niaidbioit<https://twitter.com/niaidbioit> , >@NIH3Dprint<https://twitter.com/nih3dprint> > >Disclaimer: The information in this e-mail and any of its attachments is >confidential and may contain sensitive information. It should not be used >by anyone who is not the original intended recipient. If you have >received this e-mail in error please inform the sender and delete it from >your mailbox or any other storage devices. National Institute of Allergy >and Infectious Diseases shall not accept liability for any statements >made that are sender's own and not expressly made on behalf of the NIAID >by one of its representatives. > >_______________________________________________ >Chimera-users mailing list >Chimera-users(a)cgl.ucsf.edu >http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Chimera-users March 2015