October 2003 - Chimera-dev - RBVI Mailing Lists

Comments about the release notes for linux
by David E. Konerding 05 Nov '03

05 Nov '03

Some of the release notes for linux are out of date and/or incorrect. First, the linux release notes say it was compiled on 7.1 and runs on a range of systems. That's fine, but the 'Platform' is listed as 'Red Hat 8.0', which should be 7.1. Next, your comments on Mesa have problems. The instructions say that 4.0.4 is the latest stable and the development tree is 4.1, and doesn't work. However, I tested 4.0.4, and there are numerous visual errors on my system such as bonds appearing/disappearing during molecule rotation, 4.0.1 does NOT have these problems. Also, 5.0 is the current stable branch, not 4, and has been since November of last year. I haven't tested 5.0, however, so I can't make any comments on its suitability. Dave

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AddH etc.
by Elaine Meng 24 Oct '03

24 Oct '03

Hi Timm, Thanks for the compliments! Chimera is under active development, and some of your suggestions are already on the "to do" list. (1) The best news first: atom deletion has already been incorporated and is now available in the snapshot version created earlier this month (can be downloaded by following links from the Chimera home page). You may wish to wait for the full production release, however, since we plan to make one next week. How to delete atoms: either use the menu item Actions... Atoms/Bonds... delete to delete the currently selected atoms (careful!) or the command delete [atom-spec] for example, delete element.H (delete all hydrogens) This example also shows that atom specifications have been made more powerful. In the newer (October 2003) versions, you can use several menu items under Select (such as "element.H", the entry H under Select... Chemistry... element, or even just "H") as atom specifications. Atom deletion is also really useful when you want to get rid of solvent or extra chains that you are not going to look at. (2) Coming soon: consideration of metal coordination and H-bonding networks when hydrogens are added (AddH). We will note your e-mail address (Timm) and let you know when this is available in a snapshot version of Chimera. (3) On the "to do" list, but long-term: simple molecule editing (building) and minimization capabilities. I know I'd like to do these things, but adding them is nontrivial. Thanks for your comments, 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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AddH
by Timm Essigke 24 Oct '03

24 Oct '03

Dear Chimera-Developers, I am a new user and I am amazed of chimeras great functionality! I had some problem with adding hydrogens to a iron-sulfur center containing protein. The Cys ligating the iron got protonated. I was wondering if there is an option to define additional bonds which would help to guide the hydrogen placeing algorithm, which seems to work extremely well otherwise. Also an option to delete or add atoms (particularly hydrogens) would be nice for non-standard protonation states. This might be extensible to some molecular editor, but I guess this would be a major change/new module to the program. Also some function would be nice to optimize the hydrogen bond network (either simple minimization or better some global optimization). Maybe some of the features I am looking for are there, but I couldn't find them yet... :-) Thanks for the great program! Timm Essigke

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Re: Chimera and lighting
by Thomas Goddard 23 Oct '03

23 Oct '03

Hi Steve, The SimpleSession.oslMap() call is not available in Chimera 1.1846. There is something similar SimpleSession.modelMap which can be used to emulate oslMap(). I successfully restored an EMANimator session in Chimera 1.1846 after defining in the IDLE shell: def osl_map(model_id_string): id = int(model_id_string[1:]) import SimpleSession # modelMap is a dictionary mapping (id,subid) to a list of models. m = SimpleSession.modelMap[(id, 0)][0] return '#%d' % m.id import SimpleSession SimpleSession.oslMap = osl_map You can use this trick to open your existing session files. I suggest you change your EMANimator session saving code to make it immune from these SimpleSession API changes. Then you might open old session files as above, and save them in the improved format. Unfortunately the SimpleSession state saving is tricky because of the need for backwards compatibility. I do not know which SimpleSession APIs are guaranteed to exist in all future Chimera versions. To deal with this in my volume viewer session code, I do not put any SimpleSession calls in the actual session file. Instead I save all state data in dictionaries and tuples and such, and then call a restore routine in the volume viewer module. That routine then uses whatever SimpleSession calls are needed (like oslMap). This way I can adapt the session restore code without modifying any session files. Another suggestion is to put all your session file code in a function and after that call the function in a try / except block. def restore_volume_viewer(): volume_viewer_state = {...} VolumeViewer.session.restore_volume_state(volume_viewer_state) try: restore_volume_viewer() except: reportRestoreError('Error restoring volume viewer') This minimizes namespace polution in the session file, and will allow other parts of the session restore to work if your part fails. I played with EMANimator last week and figured it all out I think. I was amazed you figured out the SimpleSession stuff for saving state. Tom ----------- Here's an example of volume viewer session file code. def restore_volume_viewer(): volume_viewer_state = \ { 'adjust_camera': 0, 'auto_show_subregion': 0, 'box_padding': '0', 'class': 'Volume_Dialog_State', 'data_cache_size': '32', 'data_panel_shown': 0, 'data_set_states': [ { 'class': 'Data_Set_State', 'data_region_state': [ { 'class': 'Data_Region_State', 'component_display_parameters': [ { 'class': 'Component_Display_Parameters_State', 'default_rgba': ( 1, 1, 1, 1, ), 'hidden': 0, 'solid_brightness_factor': 1.0, 'solid_colors': [ ( 1, 1, 1, 1, ), ( 1, 1, 1, 1, ), ], 'solid_levels': [ ( 2.8447514853193487, 0, ), ( 3.5993542671203613, 1, ), ], 'surface_brightness_factor': 1.0, 'surface_colors': [ ( 1.0, 1.0, 1.0, 1.0, ), ], 'surface_levels': [ 2.4433076821628106, ], 'transparency_depth': 0.047138079248299998, 'transparency_factor': 0.0, 'version': 1, }, ], 'name': '', 'region': ( [ 0, 0, 0, ], [ 49, 49, 49, ], [ 1, 1, 1, ], ), 'region_list': { 'class': 'Region_List_State', 'current_index': 0, 'named_regions': [ ], 'region_list': [ ( ( 0, 0, 0, ), ( 49, 49, 49, ), ), ], 'version': 1, }, 'rendering_options': { 'bt_correction': 0, 'class': 'Rendering_Options_State', 'colormap_size': 256, 'dim_transparency': 0, 'flip_normals': 1, 'line_thickness': 1, 'linear_interpolation': 1, 'maximum_intensity_projection': 0, 'mesh_lighting': 1, 'minimal_texture_memory': 0, 'outline_box_rgb': ( 1, 1, 1, ), 'show_outline_box': 0, 'smooth_lines': 0, 'two_sided_lighting': 1, 'use_2d_textures': 1, 'use_colormap': 1, 'version': 1, }, 'representation': 'surface', 'solid_model': None, 'surface_model': { 'active': 1, 'class': 'Model_State', 'display': 1, 'id': 0, 'name': 'groel.mrc', 'osl_identifier': '#0', 'subid': 0, 'version': 2, 'xform': { 'class': 'Xform_State', 'rotation_angle': 1.538469230769508, 'rotation_axis': ( 0.5773502691895197, 0.5773502691895197, 0.5773502691895197, ), 'translation': ( 0.0, 0.0, 0.0, ), 'version': 1, }, }, 'version': 2, }, ], 'data_state': { 'available_subsamplings': {}, 'class': 'Data_State', 'file_type': 'mrc', 'path': '/usr/local/src/chimera-demos/volume/examples/groel.mrc', 'version': 1, 'xyz_origin': [ -24.5, -24.5, -24.5, ], 'xyz_step': [ 1.0, 1.0, 1.0, ], }, 'name': 'groel.mrc', 'version': 1, }, ], 'display_panel_shown': 1, 'focus_region_name': '', 'geometry': '537x358+200+633', 'immediate_update': 1, 'is_visible': 1, 'limit_voxel_count': 1, 'no_colormap_multi_component_data': 1, 'options_panel_shown': 0, 'region_panel_shown': 0, 'representation': 'surface', 'selectable_subregions': 0, 'show_atom_box_button': 0, 'show_bounds': 0, 'show_named_regions': 0, 'show_on_open': 1, 'subregion_button': 'button 2', 'version': 4, 'voxel_limit': '1', 'voxel_limit_for_open': '1', } import VolumeViewer.session VolumeViewer.session.restore_volume_state(volume_viewer_state) try: restore_volume_viewer() except: reportRestoreError('Error restoring volume viewer')

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[chimera-dev] [stevel@blake.3dem.bioch.bcm.tmc.edu: Re: Colormap surfaces]
by Thomas Goddard 22 Oct '03

22 Oct '03

Steve Ludke requests a Chimera source code release because the developer documentation is inadequate. Tom ------- Start of forwarded message ------- Date: Wed, 22 Oct 2003 12:42:35 -0500 (CDT) From: Steve Ludtke To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: Re: Colormap surfaces In-Reply-To: <200310221606.h9MG6Jit1046634(a)adenine.cgl.ucsf.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII Hi. Actually, I already understood most of what you've got below. What I'm having trouble with is figuring out how to access and iterate over the elements of an existing isosurface. Again, this is a problem with the relevant part of the API being in the C source which I don't have access to. While the headers you sent before do help a bit, they aren't quite transparent by themselves. I really wish you guys would consider some sort of source release, not so we can change the source, but so we can use it as documentation... cheers... ------- End of forwarded message -------

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differences between Radeon 9800 pro and 9600 pro
by Tom Ferrin 21 Oct '03

21 Oct '03

I looked around the ATI web site. The 9600 pro and 9800 pro are definitely based on the same chip set and have very similar specs. The differences are: 9600 pro 9800 pro ======== ======== memory 64MB 128MB (the 64MB seems unique to Apple) memory interface 128-bit 256-bit rendering pipelines 4 8 pixel fill rate 1.6Gp/s 3.04Gp/s engine clock 400Mhz 380Mhz (yes, i know this seems reversed) memory clock 600Mhz 680Mhz --tom

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Fwd: [chimera-dev] database access
by Daniel Greenblatt 12 Oct '03

12 Oct '03

Hi Lars Currently, Chimera does not have any functionality that interfaces directly with MySQL-type relational databases, although this will eventually be implemented as part of another project (but not for a while still:-). However, Python *does* have several modules devoted to accessing databases, and one could write an extension to Chimera to accomplish this. We would certainly be willing to assist you in the Chimera-side development of such an extension if this is the approach you ultimately decide to take. See here for more information: http://www.python.org/topics/database/modules.html I think that all three approaches you detail are very reasonable. There are generally two ways to create a model in Chimera. The first is by reading in a known file format (such as PDB or mol2), and the second is by manually building the model from raw information. It seems that your (1) and (3) take the first approach - the server side (i.e. your database) is responsible for processing the raw information and giving Chimera a file in a format it understands. Your method (2) takes the other approach, by supplying Chimera with raw information, which it then builds into a model. This is also possible in Chimera, although this all happens in the C++ code, which is not distributed with Chimera. We don't currently have any examples illustrating this in our Programmers Guide, but if you decided to pursue this route, we could provide you with some instructional examples on how to do this. It is hard to say which one of these approaches is best, because it depends on your aims - speed/efficiency? ease of implementation? Dan Greenblatt Computer Graphics Lab University of California, San Francisco dan(a)cgl.ucsf.edu > first) > > My plugin accesses the db and creates a temporary file - then it tells > chimera to load it. > Advantage chimera can use it native (and probably fast) reading > routines... > > > second) > > The plugin fetches the data form the db and builds up the molecule in > chimera by use of the python-interface... > > > third() > > I tell chimera to access the database X, use password Y, and run > select / > or call a stored procedure. > the stored-procedure or (for older mysql a linked extension function) > could build up an input-format chimera understands from the actual > data. > the select-version would be a bit ugly cause we would need several of > them > or place some file-blobs in the bd. > > > I hope your are interested to do some thing about approach three... > > Sincerely > Lars > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev >

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thread-communication
by Lars Kunert 12 Oct '03

12 Oct '03

Hi! When my plugin talks with chimera, it does so from a foreign thread. I am currently using an approach I have "stolen" from the DelphiViewer-plugin which fetches the see __init__.py>> self.parent = chimera.tkgui.app gui-thread and places a callback see __init__.py>> self.parent.after(100, self.CheckProcess) I have added a queue in between, so my extension feeds the queue, which the gui-thread is frequently asked to process (and empty) What I actually want to know is if there some kind of functionality like this already in chimera: The programmer of the DelphiViewer suspected something like that in the trigger-stuff __init__.py: # modify this to use the chimera.triggerSet? but I can not find any threading stuff there, just plain single-thread-callbacks......or am I wrong Thank for your help Lars

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loading files
by Lars Kunert 12 Oct '03

12 Oct '03

Hi! First of all thanks for your replies to my previous questions, they were really great! when i open a file (mol2) with openmodel... how do I influence into which slot/subslot ( I suppose that are not the right terms, but I hope you know what I mean) the molecule (molecules) are loaded. I want something that loads mol2-file containing one molecule into slot X subslot Y and a multimol2 file containing Z molecules into slot X starting at subslot Y How do I delete a model (or one specific molecule in a model) from a slot (subslot) - ( by slot/subslot - numbers and/or by name)? Thanks for your help Lars

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sideview eye positioning
by Tom Ferrin 12 Oct '03

12 Oct '03

Greg, During a demo at the "visualization of large complexes" workshop that Tom Goddard and I attended this weekend, I tried to zoom in close to a single protein within bluetongue virus. But what happened was that the eye position ended up behind the yon clipping plane, and the virus particle suddenly shrunk to a tiny dot. It was not easy to get back to the previous display without opening a command line window and doing a "reset." Can't 'unreasonable' eye positions be prohibited within sideview? --tom

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