- Chimera-users - RBVI Mailing Lists

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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