- Chimera-users - RBVI Mailing Lists

Opening Gromacs .trr: error with "bham_lr"
by Alan Manning 03 Apr '15

03 Apr '15

Hi I want to import a Gromacs trajectory (a .trr file) in order to create an animation. I'm using the "MD Movie" tool, and I specify the input .tpr and .trr files. However, I get the following error when I try and make the movie: Don't know correct parameters for 'bham_lr' function Does anyone know what this is from? I'm using Gromacs 5.0.4. The complete Reply Log is as follows: using memory mapping VERSION 5.0.4 using floats version 100, generation 26 2613 atoms box o water Don't know correct parameters for 'bham_lr' function Thanks! Regards, Alan Manning

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drawing ribbon
by Hartzell Jr., Criss 03 Apr '15

03 Apr '15

I have a protein with 10 transmembrane domains and would like to make a movie in which the ribbon is drawn in time from the N- to the C- terminus. I wrote a script that does that. But, the 10 transmembrane domains become hard see because they overlap one another. To solve this problem, I wanted to make the first 600 amino acids become 70% transparent after they had been drawn. Then the drawing would continue with the second half of the protein with no transparency. The problem is that the script that I have written to do this draws the first 600 amino acids 70% transparent immediately as they are drawn. Then the second half of the protein is drawn with 0 transparency. I set the wait time to 600 because I want to execute the transparecny command after the first 600 amino acids were drawn. But, instead, the drawing of the first 600 amino acids is tremendously slowed down by this command as if a wait of some duration occurs after each amino acid rather than after all 600 amino acids. I would appreciate your help. Thanks. movie record supersample 4; perframe "ribbon #2:$1" range 1,600; wait 600; transparency 70,r #2:1-600; perframe "ribbon #2:$1" range 601,959; movie stop; movie encode “d:\Dropbox\Chimera_files\movie1.mp4”; Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322 404-242-5719 (cell) For Fedex, UPS, other courier: Criss Hartzell 615 Michael St. 535 Whitehead Building Emory University Atlanta, GA 30322 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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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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select by color (or other display attributes)
by Oliver Clarke 03 Apr '15

03 Apr '15

Hi, one feature I would love to see in a future version of chimera is the capacity to select residues/atoms by color - this would be magic for modifying figures. Example use case: I’ve made a figure in which some complicated selection or set of selections is colored medium blue, and another selection is colored red. I’ve saved the session for the figure, but I (stupidly)didn’t save the corresponding selections, and now I have to remember exactly what selections I used. If there was a “select by color” function, I could simply select all the atoms that are colored medium blue (or some other color ID), and change them to another color, without having to know which residues were in the original selection. Analagously, it would also be handy, although less frequently useful, to be able to select on the basis of whether a residue is displayed, or represented in a particular manner - in particular, being able to restrict selection to displayed atoms/residues would be useful to avoid inadvertent modification of undisplayed models or parts thereof. Cheers, Oliver.

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Smoothly change level of density map in animation?
by Oliver Clarke 02 Apr '15

02 Apr '15

Is there any way to alter the density level in a gradual fashion during an animation? I would like to first show the overall envelope of a cryoEM map, and then smoothly change to a higher contour level where I can see helices etc. Many other parameters, such as the presence of a MSMS surface or the position of a clipping plane, seem to automatically gradually transition between two key frames of an animation, but density level doesn’t seem to do so. Oliver.

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mclip suggestion - match to arbitrary plane
by Oliver Clarke 02 Apr '15

02 Apr '15

Hi, Currently the mclip command can be used to match a model specific clipping plane to the global near/far clipping planes, or the per model clipping plane of another model. I think it would be a handy addition to a future chimera version to be able to match the per model clipping plane to an arbitrary plane, pre-defined in axes/planes/centroids - e.g. “mclip #1 match p2” would match the per model clipping plane of model #1 to the plane named “p2”. This would be useful because it allows one to easily generate a per-model clipping plane that intersects a certain set of atoms, which also facilitates precise description of a figure. Cheers, 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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