- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] how to color ribbons?
by Elaine Meng 20 Aug '03

20 Aug '03

Hi Mario, I'll include two different ways you could do this in Chimera 1.1700: ---------------- with menu ---------------- Actions... Atoms/Bonds... hide Actions... Ribbon... show Actions... Ribbon... edged Actions... Color... white Select... Structure... secondary structure... helix Actions... Color... red Select... Structure... secondary structure... sheet Actions... Color... cyan Select... Clear selection ---------------- with commands ---------------- ~display ribbon ribrepr edged ribcolor white ribcolor red :/isHelix ribcolor cyan :/isSheet ---------------- In both approaches, first the atoms are undisplayed, then the ribbon is turned on. The step setting the ribbon type to "edged" is optional; you could use whichever ribbon type you want. Then, I make everything white before making helices red and strands cyan. The reason I don't use the turn descriptor is that it only applies to explicit PDB TURN records, whereas in most cases, the PDB only contains HELIX and SHEET records. You could just put the commands in a plain text file, for example named "sscolor.com," and then use the command "source sscolor.com" to execute all the commands in the file. (The file must be in the working directory; otherwise you will have to include the whole path in the source command.) I hope this helps! Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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how to color ribbons?
by Mario Albrecht 20 Aug '03

20 Aug '03

Hi, I'm new to Chimera but I'm missing a simple script in the menu for the normal display of ribbons. Helices in ribbons should be colored in red, strands in cyan, and the rest in white. May you provide such a script? Thank you much, Mario Albrecht

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background manipulation
by Jacob Schmidt 18 Aug '03

18 Aug '03

Greetings: Can you tell me how to completely get rid of the black background on which structures appear? As you probably know printer ink is not cheap. Thanks - Jakob Schmidt, Dept . Biochem and Cell Biol. SUNY Stony Brook

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saving partial coordinates
by Elaine Meng 21 Jul '03

21 Jul '03

Hi Mark, In the current release of Chimera: if you are on a non-Windows system, you can use the command "pdbrun" to save just the atoms that are displayed. You can see the manual page for this command by typing "help pdbrun" in the Chimera Command Line (by default, Favorites... Command Line). example: pdbrun nouser cat > myzone.pdb Pdbrun literally sends the information for only the displayed atoms in their displayed positions to another command, in this case "cat" to send the information to the file myzone.pdb. If you want the coordinates to be the same as in the original file, first use the command "reset." All the atoms should be in view (i.e. if you are zoomed in and the atoms around the periphery cannot be seen in the Chimera window, they won't be in your output file either). The command "save" (or File... Save Session As... ) doesn't save coordinates, only how they are positioned/colored/displayed, etc. In fact, restarting a saved session will use the original input file(s) for coordinates. The command "write" (same as the function "write PDB" in the Model Panel) saves coordinates into a file. However, these will save the entire coordinates whether displayed or not. If you are on Windows, I am not aware of a solution in the current release. In our working version and thus the next release (late summer or early fall, I believe) there is a delete action. This would allow you to select the atoms/bonds outside a zone, for example, and then actually delete them. (Actions... Atoms/Bonds... delete). Subsequently, a file created with "write" would only contain the atoms/bonds that had not been deleted. I hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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I Need Help!
by Mark Cunningham 20 Jul '03

20 Jul '03

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Re: ribbons, chimera, and collagen
by Eric Pettersen 18 Jul '03

18 Jul '03

Hi Randy, You can force Chimera to treat collagen as helical without too much difficulty. First, select a chain or chains (either Select...Chain, or pick an atom or atoms in the graphics window and use up-arrow several times until the chain(s) are selected). Then use the selection inspector (Tools...Inspectors...Selection Inspector, or click the button showing the selection in the lower-right part of the Chimera window). Change what is being inspected to 'Residue' and then set 'in helix' to true. The problem is that the ribbons don't look very good (they're too "twisty") because it's not an alpha helix. Maybe Conrad can suggest something. I don't have any suggestions myself (I tried making them "strands" and that was pretty twisty also). --Eric > I'm trying to make a ribbon plot of collagen using chimera, but it > doesn't > recognize collagen's secondary structure. > Can I just tell it to make a ribbon with the backbone atoms (or peptide > bonds), and not worry about what kind of secondary structure it really > is? > If so, how? > Have a nice day, > Randy

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Delphi and Chimera
by Marco Sette 09 Jul '03

09 Jul '03

Dear all, I have seen Chimera is able to create potential map using Delphi but, in your site, it is stated that this is valid only for unix systems. I have Delphi installed into windows and linux systems: it will be possible in the (near) future to run DelphiController onto these systems ? Thanks a lot for your attention, Best Regards, Marco -- Dr.Marco Sette, Ph.D. Deaprtment of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Re: [Chimera-users] Chimera - Dock grid
by Thomas Goddard 20 Jun '03

20 Jun '03

Hi Joel, The voldata.tar.gz file had a bug. I forgot to do byte swapping on the grid values. So it works on SGI and Mac or on Linux and Windows, but not both. I fixed this problem. The new code is at: http://www.cgl.ucsf.edu/home/goddard/voldata.tar.gz Tom

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Chimera - Dock grid
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi there, I'm quite impressed with chimera and its dock functionality. My query is about dock grid. I can't find any documentation about this ie what the values and their ranges represent. Also I can't seem to turn them off once they are on. And not to be too ungrateful different colours would be handy as well...how can I change those? While I'm at it is there a delete molecule button? Thanks for your help in advance joel -- ________________________________________ Joel Tyndall, PhD Research Officer http://www.imb.uq.edu.au Institute for Molecular Bioscience incorporating Centre for Drug Design and Development Centre for Cellular and Molecular Biology The University of Queensland Brisbane Australia 4072 Tel: +61 7 3346 2988 Fax: +61 7 3346 2101 email: J.Tyndall(a)imb.uq.edu.au

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denbsity maps
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi, I am using chimera to make some pictures of a model docked into a low resolution electron density map. Is there a way to make the mesh lines representing the electron density thicker? Also is it possible to have a cubic grid rather than triangles? Thankyou very much for your help. Suzanne Brewerton University of Cambridge --

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writing Mol2 format
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi David, Writing out Mol2 format can in principle be done, but there are a few caveats. If the original format is Mol2, the original information could be retained and written back out. I don't know how simple/hard this would be to implement (feel free to chime in, other members of the team). When the original format is not Mol2, there is less information in the molecule data than is needed to write the file. Chimera uses a fairly rich set of atom types, but there is still not a one-to-one relationship with all Mol2 types. One would need to create a mapping between the types. Also, I believe Chimera currently knows connectivity but not bond orders, and does not retain any point charge information. The online Chimera Programmer's Guide actually includes an example of code required to write out a mol2 file. I had forgotten about this when visiting your office earlier. It discusses a mapping between atom types (if you use this, you should examine this mapping and make sure it works the way you think it should). The example code writes out all bonds as single. Check it out: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html click the "Examples" link and then "Chimera's Object Model" This example is "writeMol2.py" If you have a molecule open in Chimera, you can view the type assignments using Actions... Label... IDATM type (version 1.1700). A listing/explanation of Chimera types can be seen at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html Best, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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denbsity maps
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi, I am using chimera to make some pictures of a model docked into a low resolution electron density map. Is there a way to make the mesh lines representing the electron density thicker? Also is it possible to have a cubic grid rather than triangles? Thankyou very much for your help. Suzanne Brewerton University of Cambridge --

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Writing to mol2
by chimera-users＠cgl.ucsf.edu 18 Jun '03

18 Jun '03

Hi, I'm one of your "neighbors" working in the Shoichet lab for the summer. I think it'd be neat if you could output in mol2 format rather than just pdb format, especially if the input is in mol2. Is this in the works? Has it already been done? Is it easy to do? David Minh

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Chimera & dock grids
by chimera-users＠cgl.ucsf.edu 18 Jun '03

18 Jun '03

Dear Dr. Tyndall, Thanks for your interest - DOCKgrid is indeed undocumented, partly because we have a much more advanced extension for viewing 3D data sets, Volume Viewer. This would let you have multiple contour surfaces or transparent solids in colors of your choosing, with interactively adjustable thresholds. The current hitch is that the DOCK grid formats have not yet been added to the Volume Viewer extension. We are actively looking into this and hope to incorporate it soon (we will let you know when this happens). I believe the values are directly those stored in the grid files, which (for dock 4 at least) are described in http://dock.compbio.ucsf.edu/dock4/html/Manual.1c.html#pgfId=850 The VDW repulsion, VDW attraction, and electrostatic grid values are described in equation 9 (all three are in the *.nrg grid). These are not in energy units until multiplied by ligand atom parameters. I believe the color choices in DOCKGrid are red and red. Display with Volume Viewer should be a vast improvement. To close molecules and also these contour surfaces, one way is to open the Model Panel (Tools... Inspectors... Model Panel in version 1.1700). In the Model Panel, choose the model(s) you want to close on the left side, then click "close" on the right side (not the Model Panel Close button). Unfortunately the contour surfaces created by DOCKgrid are each VRML files without an informative title, so it may be hard to tell which is which. If you only have one, of course, it will be obvious. I hope this helps! Best regards, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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Re: Chimera graphics card requirements
by chimera-users＠cgl.ucsf.edu 10 Jun '03

10 Jun '03

Hi Jim, I think Chimera will start without an OpenGL stencil buffer. But the outline highlighting of selected atoms/bonds/... will not work. Fill mode highlighting settable with Favorites/Preferences/General/ Selection highlight method will work. With a Quadro4 700 XGL on Linux you should definitely have a stencil buffer available. Below is the output of "glxinfo -t" on my Linux system with Quadro4 500 graphics. It shows half the visuals have 8 bit stencil buffer. It shows I am using the Nvidia 4191 driver OpenGL version string: 1.4.0 NVIDIA 41.91 Check the OpenGL version string on your machine to make sure you are using the Nvidia driver and not Mesa (software opengl). Tom $ glxinfo -t name of display: :0.0 display: :0 screen: 0 direct rendering: Yes server glx vendor string: NVIDIA Corporation server glx version string: 1.3 server glx extensions: GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer client glx vendor string: NVIDIA Corporation client glx version string: 1.3 client glx extensions: GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_EXT_import_context, GLX_SGI_video_sync, GLX_SGIX_swap_group, GLX_SGIX_swap_barrier, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_NV_float_buffer GLX extensions: GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_ARB_get_proc_address OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: Quadro4 500 GoGL/AGP/SSE2 OpenGL version string: 1.4.0 NVIDIA 41.91 OpenGL extensions: GL_ARB_imaging, GL_ARB_multitexture, GL_ARB_point_parameters, GL_ARB_texture_compression, GL_ARB_texture_cube_map, GL_ARB_texture_env_add, GL_ARB_texture_env_combine, GL_ARB_texture_env_dot3, GL_ARB_texture_mirrored_repeat, GL_ARB_transpose_matrix, GL_ARB_vertex_program, GL_ARB_window_pos, GL_S3_s3tc, GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color, GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_clip_volume_hint, GL_EXT_compiled_vertex_array, GL_EXT_draw_range_elements, GL_EXT_fog_coord, GL_EXT_multi_draw_arrays, GL_EXT_packed_pixels, GL_EXT_paletted_texture, GL_EXT_point_parameters, GL_EXT_rescale_normal, GL_EXT_secondary_color, GL_EXT_separate_specular_color, GL_EXT_shared_texture_palette, GL_EXT_stencil_wrap, GL_EXT_texture_compression_s3tc, GL_EXT_texture_cube_map, GL_EXT_texture_edge_clamp, GL_EXT_texture_env_add, GL_EXT_texture_env_combine, GL_EXT_texture_env_dot3, GL_EXT_texture_filter_anisotropic, GL_EXT_texture_lod, GL_EXT_texture_lod_bias, GL_EXT_texture_object, GL_EXT_vertex_array, GL_IBM_texture_mirrored_repeat, GL_KTX_buffer_region, GL_NV_blend_square, GL_NV_fence, GL_NV_fog_distance, GL_NV_light_max_exponent, GL_NV_packed_depth_stencil, GL_NV_pixel_data_range, GL_NV_point_sprite, GL_NV_register_combiners, GL_NV_texgen_reflection, GL_NV_texture_env_combine4, GL_NV_texture_rectangle, GL_NV_vertex_array_range, GL_NV_vertex_array_range2, GL_NV_vertex_program, GL_NV_vertex_program1_1, GL_NVX_ycrcb, GL_SGIS_generate_mipmap, GL_SGIS_multitexture, GL_SGIS_texture_lod glu version: 1.3 glu extensions: GLU_EXT_nurbs_tessellator, GLU_EXT_object_space_tess Vis Vis Visual Trans buff lev render DB ste r g b a aux dep ste accum buffers MS MS ID Depth Type parent size el type reo sz sz sz sz buf th ncl r g b a num bufs ---------------------------------------------------------------------------------------------------- 0x21 24 TrueColor 0 32 0 rgba 1 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x22 24 DirectColor 0 32 0 rgba 1 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x23 24 TrueColor 0 32 0 rgba 1 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x24 24 TrueColor 0 32 0 rgba 0 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x25 24 TrueColor 0 32 0 rgba 0 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x26 24 TrueColor 0 32 0 rgba 1 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x27 24 TrueColor 0 32 0 rgba 1 0 8 8 8 8 0 0 0 16 16 16 16 0 0 0x28 24 TrueColor 0 32 0 rgba 0 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x29 24 TrueColor 0 32 0 rgba 0 0 8 8 8 8 0 0 0 16 16 16 16 0 0 0x2a 24 DirectColor 0 32 0 rgba 1 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x2b 24 DirectColor 0 32 0 rgba 0 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x2c 24 DirectColor 0 32 0 rgba 0 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x2d 24 DirectColor 0 32 0 rgba 1 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x2e 24 DirectColor 0 32 0 rgba 1 0 8 8 8 8 0 0 0 16 16 16 16 0 0 0x2f 24 DirectColor 0 32 0 rgba 0 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x30 24 DirectColor 0 32 0 rgba 0 0 8 8 8 8 0 0 0 16 16 16 16 0 0 > From: Jim Procter <procter(a)zbh.uni-hamburg.de> > Reply-To: procter(a)zbh.uni-hamburg.de > Organization: Zentrum Bioinformatik Hamburg > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Chimera graphics card requirements > Date: Tue, 10 Jun 2003 10:53:20 +0200 > > Hi. I'm sorry to bother you again - particularly with some trivial hardware > question, but I've been wondering about the minimum specification of OpenGL > graphics driver needed for Chimera. > > We have Quadro4 700 XGL/AGP/SSE2 drivers for our linux-installations, on what > I would expect to be fairly high-end PCs. There doesn't seem to be any way to > force these drivers to generate a stencil buffer - is this what other people > have found ? > > Thanks. > Jim

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Re: Chimera at NCMI
by chimera-users＠cgl.ucsf.edu 09 May '03

09 May '03

Hi Steve, I'll ask the other Chimera developers about making independent mode rotation use the center of the whole model when it is undisplayed. Unfortunately that is a change in the C++ that would not be available for a while. I'll try making a rotation/translation undo button next week. I think it can be done all in Python and I could just email you the code. Tom > Date: Fri, 9 May 2003 20:48:49 -0500 (CDT) > From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> > Reply-To: sludtke(a)bcm.tmc.edu > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > > Yeah, a rotation/translation undo would be great! The miscentering > problem isn't an issue for what I'm doing right now (at least not much of > one, but a more generic way of setting the center would be nice. Perhaps > using the origin you set for the volume data as a center for rotation. The > manual translations seem to be independent of this value... > > cheers... > > -- > ---------------------------------------------------------------------------- > Steven Ludtke, PhD | Baylor College of Medicine > sludtke(a)bcm.tmc.edu | Co-Director > stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging > V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. > instant messenger: sludtke42 | * Those who do ARE * > http://ncmi.bcm.tmc.edu/~stevel | The converse also holds

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independent rotation mode
by chimera-users＠cgl.ucsf.edu 09 May '03

09 May '03

Date: Fri, 9 May 2003 13:57:27 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Hi again. I just ran across a bug I thought I'd report. The session file is rather large, so I won't attach it initially. Let me know if you have problems reproducing it. Anyway, I have loaded several volume data sets which represent different versions of the same structure. Then: 1) set 'independent' rotation mode 2) set one model so it is active, but not shown (in the model panel) 3) rotate the models 4) set the model in 2 to be shown again Even though it was active, the model in 2 was not rotated. I have a complex scenario of models where I need to do this operation frequently, so right now all my rotations keep getting messed up unless I make sure all the models are active AND shown before rotating anything. Cheers... PS - This happens with both the current 1700 version and the previous one. -- ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds Date: Fri, 9 May 2003 15:04:20 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Not THAT big a rush. Whenever you have a chance :^) Anyway, I was trying to avoid having to explain the whole situation, but here goes. I have a PDB model, a density map based on the PDB model and 3 different EM maps of the same molecule (each a little different). All are aligned and centered. What I want to do is have the EM map(s) with overlaid PDB structure on the left side of the screen and the x-ray map with overlaid structure on the right half of the screen. Then I use 'independent mode' to rotate everything about its own center so I can see how the EM map and x-ray map compare. As long as everything is active and displayed, it works beautifully (except the PDB model center seems very slightly off, so you see a very small amount of the centering artifact you described). Anyway, on the 'EM' side, I have 3 models overlaid. Generally I want to turn their display on and off as I rotate each one around and look at them. However, even though all 3 remain active, when I turn off the display of a model (ONLY in independent mode), it no longer gets rotated properly. Hope that helps clarify... cheers. -- ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds From: Tom Goddard The problem is that indepedent rotation mode only rotates about the the center of the displayed part of the model. If nothing is displayed there is no center to rotate about. Date: Fri, 9 May 2003 20:02:39 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> I understand. I sort of figured it was something like this. Well, I'll give you my perspective as a 'user' from the EM community. As funny as it seems, I would actually want the opposite of the behavior you stated. That is, the molecules would always rotate about their 'true' center even if part wasn't displayed. The best solution from my perspective would either A) have a different 'independent' mode where things always rotated about their true centers or B) Make it so models that aren't displayed at all use their true center. This doesn't seem quirky to me. If the model is active, you assume some sort of rotation will occur. Presumably if part of the molecule is visible, the whole thing still gets rotated, just about a different center. So, it's odd for it not to get rotated at all. >From a user perspective, a problem I keep running into is that I accidentally do a rotation when not all of the molecules are active. This produces a relative rotation that is virtually impossible to undo through the GUI. Translations aren't a problem. They're pretty easy to 'undo' almost perfectly. But rotations are really tricky. When that happens I end up having to revert to my last saved session. So, having the model not rotate at all just because it isn't visible is doubly annoying... Anyway, just my perspective... -- ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds Hi Steve, I agree it is odd for the undisplayed model not to be rotated at all. It seems reasonable that when the model is undisplayed it should use the center of the whole model if you are using independent rotation mode. There is the additional problem that the centers of the models don't coincide. When you display an isosurface, it uses the center of the bounding box that just contains the surface. It does not use the actual bounds of the whole density map. I see that Chimera has support for fixing the center of rotation for each model. This could be used to get exactly the rotation behaviour you want. But we need a user interface to let you say which models you want to group together with a common center. I could write something like this in Python. This would address both the undisplayed models not rotating, and the not quite right centers of rotation. I realize that accidentally unaligning two models in Chimera is a disaster -- it usually means starting over. I think we need a rotation and translation undo to address this. Tom

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Re: Chimera and O brix format
by chimera-users＠cgl.ucsf.edu 06 May '03

06 May '03

Hi Ed, I wrote the SPIDER volume file reader for Chimera. You can get it from http://www.cgl.ucsf.edu/home/goddard/spidervol.tar.gz and unpack it % cd /usr/local/chimera/share % tar zxf spidervol.tar.gz It includes a new VolumeData/fileformats.py that adds the SPIDER file reader to the list of supported file formats, and a VolumeData/spider directory that contains the Python code to read the data. I don't think this should be announced on the SPIDER newsgroup until we make our next Chimera release that includes it. I'd like to figure out how the spacing between grid points in physical units is handled by SPIDER. I see a "scale" parameter in the SPIDER file header, but the documentation says SPIDER does not use this, and in the file you sent me it was set to zero. Chimera likes to know the correct scale in physical units (eg angstroms or nanometers) so when a second model is opened they are drawn to the same scale. There are entry fields to hand set the scale in the Volume Viewer dialog, but it is nicer to be able to extract this from the file header. Tom

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Re: Chimera and O brix format
by chimera-users＠cgl.ucsf.edu 05 May '03

05 May '03

Hi Ed, I extended the current Chimera DSN6 file reader to handle the BRIX files. The changed files are in chimera/share/VolumeData, specifically fileformats.py and the dsn6/*.py files. Here is a tar file you can extract in chimera/share to update these files. http://www.cgl.ucsf.edu/home/goddard/voldata.tar.gz % cd /usr/local/chimera/share % tar zxf voldata.tar.gz Let me know if you have trouble with it. I have only tested it on the file you gave me. I used BRIX format documentation from the web though and expect it should work with all files. It will be included in the next Chimera release. Tom

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Strange behavior, crashing, etc.
by chimera-users＠cgl.ucsf.edu 24 Apr '03

24 Apr '03

Okay, Chimera has rather suddenly gone unstable on me. I can fully appreciate that it might be something that I've done, but I'd like some help getting it usable again. I've seen two different behaviors now. The first is that when I load a pdb file of a calcite crystal, then try to rotate the crystal... boom. Chimera crashes and everything is gone. I'm not sure if this has to do with this one file or not. In an attempt to figure that out, I relaunched Chimera and started opening files, one at a time. The first file, a small NaCl crystal, opened just fine. I could rotate it, etc. I closed it, and opened a file with graphite in it. Same thing, everything was fine. Next I opened a diamond file. This turns out to have been a big mistake. When I tried to open the diamond file, everything froze. I couldn't close any of the Chimera windows or pallets. None of the menus would respond. After waiting for a little bit, I quit X11. This successfully shut Chimera down, but there's now a new problem. When I quit X11, the Chimera icon stayed in my dock. Right clicking on it brings up the contextual menu saying that the application is not responding, but choosing 'Quit' from this menu does nothing, and Chimera doesn't show up in the Force Quit dialog. To top it all off, relaunching X11, and then double clicking on Chimera (the application, not the dock icon) does nothing. Chimera seems to be down for the count. I haven't yet tried a command-line 'kill process', or restarting. The only two major changes/additions that I've made to my computer recently are updating to Mac OS X 10.2.5, and installing Fink. On a rather unrelated note, Chimera behaves very strangely if you Hide X11 while Chimera is running. All of the pallets simply have their title bars vanish, making it very difficult to work with them. I've gotten past this by using multiple desktops, but being able to hide an application while working in another is a valuable feature, and I'd like to see the proper functionality established, if that's possible. Geoff.

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Re: [chimera-dev] Strange behavior, crashing, etc.
by chimera-users＠cgl.ucsf.edu 24 Apr '03

24 Apr '03

Hi Geoff, Eric Pettersen tells me Chimera is hanging when you display diamond.pdb in ball and stick or sphere mode because it is searching for rings. There are too many rings to find. Eric will look at fixing the ring finding code. The reason it needs to know the rings for some display modes is so it can identify atom types (classed by connectivity) so it can assign correct atom radii. You can work around the problem by issuing a Chimera command to set the vdw radii before using ball and stick or sphere display. Use Favorites/Command Line and type a command like vdwdefine * * 1.0 This example sets all atom radii to 1 angstrom (for sphere display). See the User's Guide under Commands for details on setting the radii of specific atoms if you want different atoms shown with different sizes. Any application, Aqua or not, can have an icon in the Dock -- it just has to be packaged with the Mac App directory layout and have an icon file. But Force Quit apparently only lists Aqua applications. The Aqua version of Chimera is shown in the Force Quit list. Tom

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Re: [chimera-dev] Strange behavior, crashing, etc.
by chimera-users＠cgl.ucsf.edu 24 Apr '03

24 Apr '03

Hi Geoff, Chimera freezes up for me after I open diamond.pdb and then try to show it as ball and stick or sphere. It doesn't freeze up with wire display style. When it freezes I use: % ps -xwww | grep python2.2 3676 ?? R 0:44.37 /Users/goddard/Applications/Chimera-X11-1700.app/Contents/Resources/bin/python2.2 /Users/goddard/Applications/Chimera-X11-1700.app/Contents/Resources/share/__main__.pyp % kill 3676 The Chimera executable is python2.2 and this just kills Chimera, not the X server. It doesn't appear in the Force Quit dialog because it is not a native Aqua windows application. Are you using Chimera build 1700 (March 27, 2003)? The Chimera Help/Version Info menu entry will tell you which version you have. I'll look into why Chimera 1700 is freezing on diamond.pdb. Tom

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Re: [chimera-dev] Mailing list, etc.?
by chimera-users＠cgl.ucsf.edu 08 Apr '03

08 Apr '03

> Now to a comment. After some tinkering, I finally managed to output a > new PDB file that contained models from several other PDB files. This, > however, wasn't exactly an easy of intuitive thing to do. My first > thought had been to use the 'Write PDB' command in the Model Panel. > However, that button automatically greys itself out when more than one > model is selected. I finally stumbled upon the command line command > 'pdbrun cat > file'. So, I was able to do what I wanted, but I had to > go through a rather backdoor method. Any chance that things like > 'Write PDB' will be enabled when more than one model is selected? I could enable 'write PDB' with multiple models selected. I guess my question is why do you want multiple PDB models in a single file? What will you do with that file? Knowing how you want to use the file will help me decide if simply enabling the button is the way to go or if some other interface is more appropriate. If I enabled it, the models would be separated by END records. > And what about a method of adding more atoms, other than just > hydrogen? (I also know of 'backdoor' ways that I can do this, but I'd > love to see Chimera become a more fully featured molecular modeler, and > to that end, I'm quite happy to give all kinds of input.) I'm currently working on smarter hydrogen addition (avoiding steric conflicts and maintaining hydrogen-bonding interactions). I should be done with that in time for our next release. I intend to work on some limited structure-building features after that. So a preliminary version might be available two releases from now. Even I'm not aware of backdoor ways to add non-hydrogen atoms! I guess the swapaa command _sort_ of does this, but it's not at all generic. Are you writing Python code to do this? Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Re: [chimera-dev] Mailing list, etc.?
by chimera-users＠cgl.ucsf.edu 07 Apr '03

07 Apr '03

On Monday, April 7, 2003, at 10:06 AM, Thomas Goddard wrote: > Now to a comment. After some tinkering, I finally managed to output a > new PDB file that contained models from several other PDB files. This, > however, wasn't exactly an easy of intuitive thing to do. My first > thought had been to use the 'Write PDB' command in the Model Panel. > However, that button automatically greys itself out when more than one > model is selected. I finally stumbled upon the command line command > 'pdbrun cat > file'. So, I was able to do what I wanted, but I had to > go through a rather backdoor method. Any chance that things like > 'Write PDB' will be enabled when more than one model is selected? > And what about a method of adding more atoms, other than just > hydrogen? (I also know of 'backdoor' ways that I can do this, but I'd > love to see Chimera become a more fully featured molecular modeler, and > to that end, I'm quite happy to give all kinds of input.)

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