- Chimera-users - RBVI Mailing Lists

DTI stereo3D
by Dougherty, Matthew T 06 Apr '15

06 Apr '15

?When selecting DTI stereo3D, L&R images are placed side by side, and horizontally rescaled by half, known as SBS-half. I would like to generate SBS-full, ie no horizontal scaling. Is there a way to do that in chimera? Would prefer not to generate stereo pairs and rescale them back to 100% using a video editor. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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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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Autodock vine problem
by Tunc Morova 04 Apr '15

04 Apr '15

Hello, I was trying to use built-in auto dock vina tool of chimera. I came a cross with an error saying service local`c:\”program filex(x86)”\”the scripps research Institute\Vina\Vina.exe` is unavailable. I have been checking forums for a longtime. Unfortunately, i couldn’t run the docking. couple days ago, I think i accidentally ran the docking locally but i am not sure. Is my pathing correct? how can my local auto dock vina be unavaible ? Please help me for finishing my thesis :D Thank you for your support -Tunc

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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 02 Apr '15

02 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 01 Apr '15

01 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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Rename models from command line
by Oliver Clarke 30 Mar '15

30 Mar '15

Hi all, Is there any way to rename models from the command line? I can do so using the model panel, but I have a script that generates a bunch of different models, and I would like to give them descriptive names apart from the model id in the script. Oliver.

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MatchMaker-vs-MatchAlign
by Egor Tchesnokov 30 Mar '15

30 Mar '15

Hello, 1. I used MatchMaker to align two structures, worked well and I got an alignment file-1. Then I clicked on MatchAlign and got alignment file-2. The alignment-1 is different from alignment-2. Could you please let me know what is the differnce between MatchMaker and MatchAlign? 2. In the same function I can't find RR distance map. Is it applicable to MatchMaker/MatchAlign? Thank you Egor

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on the section command
by Smith Liu 30 Mar '15

30 Mar '15

Dear All, Wil you please tell me how can I stop or pause the movie playing as a specific point which I want to watch carefully when the section command is in the execution? Smith

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Running graphical Chimera from remote server
by Hurt, Darrell (NIH/NIAID) [E] 29 Mar '15

29 Mar '15

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.html 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.…> 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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Tutorials
by Bobby Barnett 28 Mar '15

28 Mar '15

I was wondering if anyone had interactive tutorial session(s) that can be used to educate a small class of undergraduate students. Bobby Barnett Department of Chemistry University of Chemistry

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Problems with reproducing 'write relative' output
by Dan McNamara 25 Mar '15

25 Mar '15

Hi all, I am encountering a strange inconsistency with the 'relative' option for the "write" command. Searching for similar problems on the mailing list came up short, so I thought I'd ask about it. To put it briefly, I run chimera with --nogui and perform ~780,000 total matches in which I write out new coordinates using 'relative.' My issue lies in automating this process with .com scripts, which creates different results from typing out the exact same commands into the command line of the GUI. This has been plaguing me for a year or so, and most recently I can cite using version 1.10.1 (build 40427). Below is a small example to illustrate my operations. The "B-new_#.pdb" output files will contain different coordinates if they originate from automated runs or manual execution. This problem is sporadic and I cannot narrow down the source of the discrepancy. From best I can tell, there are occasionally output files from automation (e.g. B-new_#.pdb) that are in the correct coordinate reference frame. However, many (most?) are not and it is a big obstacle. I hope that someone may have some insight on this problem. /////////// example /////////// open A.pdb open B.pdb open C.pdb ##write out selection from #0 [this file is always consistent] select #0:... write selected relative 0 #0 A-new.pdb ##move #2 onto #0 match #2:... #0:... ##move #1 onto #2 match #1:... #2:... ##write out selection from #1 and save it in its new position relative to #0 [inconsistent] select #1:... write selected relative 0 #1 B-new_1.pdb ~select all ##move #1 slightly match #1:... #2:...+1 ##write out selection from #1 and save it in its new position relative to #0 [inconsistent] select #1:... write selected relative 0 #1 B-new_2.pdb ~select all ##move #1 slightly more match #1:... #2:...+2 ##write out selection from #1 and save it in its new position relative to #0 [inconsistent] select #1:... write selected relative 0 #1 B-new_3.pdb /////////// example /////////// Best, Dan McNamara

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black bar in saved image
by sunyeping 25 Mar '15

25 Mar '15

Dear all,I find in the saved volume image (png file), there are some black bar whick mask the image? Please see the following link:https://www.dropbox.com/s/nvy3douvafymqxd/image.png?dl=0Do you know how to get rid of them?Thank you very much! Yeping Sun Institute of Microbiology, Chinese Academy of Sciences

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Creating MultiScale surface from a script
by Cruz, Phil (NIH/NIAID) [C] 24 Mar '15

24 Mar '15

Hello Chimera users, I need to create a MultiScale surface from a Chimera python script when the model is of large structures such as virus particles. On a Mac, the following lines work great: import MultiScale d = MultiScale.show_multiscale_model_dialog() d.make_multimers_cb(molecules=None) and produce the desired surface output. Unfortunately, where I really need this to work is on a Linux server using the special version of Chimera that doesn't require a graphics head. When I run the script there I get errors, presumably when the script tries to create the dialog: Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.10.1/share/chimeraInit.py", line 698, in init midas_text.doRunScript("runscript", script) File "/opt/UCSF/Chimera64-1.10.1/share/Midas/midas_text.py", line 2206, in doRunScript execfile(scriptPath, scriptGlobals) File "Chimera_Molecular.py", line 301, in <module> d = MultiScale.show_multiscale_model_dialog() File "/opt/UCSF/Chimera64-1.10.1/share/MultiScale/__init__.py", line 2296, in show_multiscale_model_dialog return dialogs.display(MultiScale_Model_Dialog.name) File "/opt/UCSF/Chimera64-1.10.1/share/chimera/dialogs.py", line 76, in display dialog = find(name, create=1) File "/opt/UCSF/Chimera64-1.10.1/share/chimera/dialogs.py", line 61, in find return d() File "/opt/UCSF/Chimera64-1.10.1/share/chimera/baseDialog.py", line 665, in __init__ from tkgui import windowSystem File "/opt/UCSF/Chimera64-1.10.1/share/chimera/tkgui.py", line 73, in <module> import Togl ImportError: No module named Togl Is there a way to have the script create the multiscale surface without invoking the dialog (if that's what the issue is), or some other approach to get this to work in the required environment? Thanks for any suggestions. -- Phillip Cruz, Ph.D. Contractor, Medical Science & Computing Computational Structural Biologist Computational Biology Section Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Dr., Room 3B62 Bethesda, MD 20892-0485 Office: 301-451-1089 http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/> (Within NIH) http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public) 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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command related to the alignment of the ribbon form and the ball & stick form
by Smith Liu 24 Mar '15

24 Mar '15

Dear All, If by Chimera we open a PDB and a corresponding mrc file, and we display the molecule by both ribbon format and ball & stick format, we can find there is a minor disalignment between the ribbon representation and the ball & stick representation. I remember I have read somewhere by a ribbon related command the Chimera can align the ribbon representation and ball & stick presentation nicely, but I have forgotten where I read the tutorial or introduction. Will you please tell me the command to have chimera to get good alignment of the ribbon representation and ball & stick presentation, or tell me the weblink of the corresponding tutorial or reference? I am looking forward to getting your reply. Smith

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Sampling the density of a map in the vicinity of each atom in a model
by Mario J. Borgnia 23 Mar '15

23 Mar '15

Hi, I have a density map in mrc format and a model in pdb format. I would like to calculate the average density within a 3D window centered at the coordinates of each atom in the model and include the result as an attribute for the atom. Despite some effort searching for the answer, I cannot find out how to do this easily. I could try and go deep into Python programming but, before I reinvent the wheel, I'd like to know whether there already is a simpler way to do this in Chimera. Thanks! Mario -- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia(a)nih.gov | +---------------------------------+

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Re: [Chimera-users] Query on morph command in Chimera
by Elaine Meng 22 Mar '15

22 Mar '15

On Mar 22, 2015, at 9:38 AM, vinothkumar <vkumar(a)mrc-lmb.cam.ac.uk> wrote: > Dear Elaine, > I have three different volumes/maps of the same protein but differing in conformation. I am able to use the command line - ‘vop morph #0,1,2 constantVolume True model #3 frames 200’ which then interpolates and I could produce a movie. However, by default the threshold for the volumes and level goes to 4. Is there a way to insert in the command line to tell that all the volumes be set to level (1) and a certain threshold. > Thank you > Regards > Vinoth Dear Vinoth, You should adjust the threshold of the maps before the morphing. This could be done with the “volume” command if you are not using GUIs, e.g. command: volume all level 1 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general> Actually, my own experiments suggest it is only the threshold of the first input map that matters in setting the starting level of the morph. If you use the “constantVolume” morphing option, however, the threshold will be adjusted to keep the enclosed volume constant. If you really wanted to keep it exactly at 1 through the whole morph, you would not use that option. I hope this helps! For future questions, we recommend you send them to chimera-users(a)cgl.ucsf.edu (CC’d here) instead of to me or other individuals directly, unless you are including private data. 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

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problem related to open the chimera file by Coot
by Smith Liu 21 Mar '15

21 Mar '15

Dear All, I have fit a PDB file with a MRC by the Chimera. I saved both the fitted PDB file and the fitted MRC file by coot. When I open the fitted PDB file and the fitted MRC file by Chimera at the same time, they still fit perfectly. However when I open the Chimera fitted PDB file and the Chimera fitted MRC file by coot, the protein backbone (and the sidechains) does not fit the MRC file anymore. Will you please tell me what should I do in order to have the Chimera fitted PDB file and the Chimera fitted MRC file still fit in Coot? I am looking forward to getting your reply. Smith

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