- Chimera-dev - RBVI Mailing Lists

Re: [Chimera-users] chimera in fink
by Eric Pettersen 15 Sep '04

15 Sep '04

On Sep 14, 2004, at 4:42 PM, Grant Jacobs wrote: > > FWIW, I prefer the .dmg style installer, or at least single package, > one click installers. Its also useful to have the application > relocatable to any folder within /Applications. Certainly if you're _not_ using fink, the .dmg is almost certainly what you want. I find it highly convenient too. If you're using fink, perhaps you'd like to be able to do everything through that mechanism, but as you point out sometimes even fink users prefer the .dmg install. And given the work we would need to do before we could even try to have Chimera available via fink, it won't be happening soon. >> We haven't really seriously considered it, no. One stumbling block >> is that Chimera really isn't completely open source yet. We >> distribute the source to the Python part of Chimera but not the C++ >> part. We plan on distributing the C++ part once we have organized it >> enough that outside developers would have a prayer of compiling it, > > :-) > > For my money I'd be more concerned about good documentation of the > APIs (etc) so that people can build on what already exists without > having to decipher someone else's code base. Just my 2c - my pet peeve > about open source is that poor or non-existant documentation forces > everyone up the same time-wasting learning curves. > >> but we haven't put in the work to do that yet -- always so many >> things to do! Yes, better documentation would be part of "organizing" the C++ part. Right now, the only comprehensive API documentation we have is the programmer's reference guide, which amounts to simply a dump of all APIs with some doc strings thrown in -- barely more useful that using 'dir' on Python objects of interest. The best documentation we have is the programmer's examples, which do a good job of explaining how to do various commonly-desired tasks in Chimera, such as getting your extension into the menus, using molecular data, and saving into sessions. Once you want to go beyond the realm of the examples, we trust that people will look at other Chimera extensions that do similar things to what they want to do and figure things out. It's the best we have until we get that "organizing" done. Of course, we do answer any development-related questions we get on chimera-dev(a)cgl.ucsf.edu. The other thing about a documented API is that you can expect that it won't disappear from one release to the next -- at least not without a migration path being provided. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Chimera programming in Solaris
by Hongbo Zhu 03 Sep '04

03 Sep '04

Hi, I want to include Chimera python packages in my program under Solaris. Concretely, I want to use the UnitCell-related packages to construct the crystal unit cell from PDB files. I read through the mailing list and I know it's not possible to get chimera for solaris now. But is there any other method I can use to invoke related packages, e.g. import chimera, in my python program in solaris? Thanks in advance! -- Macro Zhu macrozhu(a)gmail.com

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by Sheetal Patil 03 Sep '04

03 Sep '04

Hello, Iam trying to configure Phantom desktop with Chimera. I get the following error: "Couldnot load Chimers_phantomcursor library.Can you please tell me where I can find this piece of software? Thanks, Sheetal +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ " The future belongs to those, who believe in the beauty of their dreams "

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adding commands
by Eric Pettersen 27 Aug '04

27 Aug '04

I added an example ("Adding Command-line Commands") to Chimera's programmer examples describing how to add your own commands to Chimera's command-line interpreter. The functionality described in the example will not be available until the next Chimera release, in 2-6 weeks. The programming examples are at http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/ index.html Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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emulating the command line change
by Eric Pettersen 13 Jul '04

13 Jul '04

Hi, Just wanted to note that Midas.midas_text.makeCommand() is changing (it is used to emulate typed commands). It now immediately executes the relevant functionality instead of returning a string that can be exec'ed. So when this change becomes available in the next release, alter your code that uses makeCommand() to just call it directly instead of exec'ing what it returns. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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regd error when opening a .mrc file
by Sandeep N Seshadri 30 Jun '04

30 Jun '04

i am getting the following error when i try to open a .mrc file . i generated a .pdb file and use a pdb2mrc to generate a .mrc file . i tried opening the .pdb file it works fine but when i try to open the .mrc file it gives the error. if anyone has any idea on why this error occurs please let me know thanks sandeep Error while processing test-helix.mrc: ZeroDivisionError: float division (see reply log for Python traceback info) Traceback (most recent call last): File "/home/sandeep/chimera/share/__main__.py", line 56, in ? value = chimeraInit.init(sys.argv) File "/home/sandeep/chimera/share/chimeraInit.py", line 275, in init prefixableType=1) File "/home/sandeep/chimera/share/chimera/__init__.py", line 886, in open models = func(filename, *args, **kw) File "/home/sandeep/chimera/share/VolumeViewer/ChimeraExtension.py", line 30, in open_cb d.add_data_sets([g]) File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 175, in add_data_sets self.redisplay_cb() File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 459, in redisplay_cb self.show_using_dialog_settings(self.focus_region) File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 380, in show_using_dialog_settings tp.update_histograms(data_region) File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 1142, in update_histograms cw.update_histogram(data_region, read_matrix, self.dialog.message) File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 1465, in update_histogram h.show_data(Numeric.log(s.counts + 1)) File "/home/sandeep/chimera/share/VolumeViewer/histogram.py", line 26, in show_data hscale = float(cheight) / max_height ZeroDivisionError: float division

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JPEG image format
by Greg Couch 24 Apr '04

24 Apr '04

I hate to suggest this, but we should consider dropping support for the JPEG image format to avoid liability due to possible patent infringement. We can reinstate JPEG support in 2007 after the patent expires. See <http://www.eweek.com/article2/0,1759,1572333,00.asp>. I agree that it is not likely that we will be sued, but the patent is now owned by a IP company (read lawyer owned and operated), so why take the risk. - Greg

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Re: [Chimera-users] compiling minrms on mac os10.2.8
by Eric Pettersen 02 Apr '04

02 Apr '04

On Friday, April 2, 2004, at 11:34 AM, Chris Adams wrote: > I am also trying to get minrms on my OS10.2.8 machine. I followed the > commands you recommended to Howard to get the "make" command to work. > However, my ls output was not at all like what you said would happen > in the message. I get this: > > ls -1 /usr/bin/*make > /usr/bin/automake One little thing is that you wanted to use the '-l' flag (lowercase L) rather than '-1' (numeral one). Nonetheless, either way this indicates that bsdmake and gnumake as well as the symbolic link from make to gnumake are missing. This indicates that the developer tools haven't been installed on your system. The developer tools came with your original installation CDs (on a separate CD) as an optional install. > and am unable to compile the minrms program. I am not very unix savvy > but am learning, perhaps you can help? You could install the developer tools and proceed from there. However, as part of the exchange with Howard I wound up compiling MinRMS myself and sending it to him. I will send you what I sent to him, but as a separate mail to avoid having the attachment sent to these lists. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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by Howard M. Fried 19 Mar '04

19 Mar '04

Hi: I'm trying to get MinRMS. I downloaded your source code but apparently my Mac with OS 10.2.8 does not have the 'make' program (I've got Developer Tools as well). My Unix-knowledgeable friend here confirmed this; he was unable to figure out how to compile MinRMS on my machine. As well, the computer support people here have been useless. Is there any way to obtain an executable version of MinRMS under X11 on Mac? Thanks, Howard Fried Dept. Biochemistry Univ. North Carolina-Chapel Hill

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Chimera on Athlon 64 / Linux
by Thomas Goddard 10 Mar '04

10 Mar '04

I compiled Chimera on an Athlon 64 processor running a 64 bit version of Linux for Steve Ludke using one of his machines. I had to fix about 20 build errors, mostly in foreign packages. There were 4 types of errors: 1) using /usr/X11R6/lib instead of /usr/X11R6/lib64 2) not using -fPIC compiler flag required for shared libraries 3) specifying -malign-double compiler option, illegal on this machine 4) g++ 3.3.1 bug related to throwing standard exceptions that generates "inconsistent operand constraints in an 'asm'". Work around by using -O2 or in some cases no -O# option I hand edited makefiles and configure scripts to make the compilation work. It took a full day. I didn't update our foreign build scripts. That would likely take a week. Since we don't have an Athlon 64 bit machine that doesn't seem worthwhile right now. Tom

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Fwd: ADC News #388
by Eric Pettersen 09 Mar '04

09 Mar '04

Kind of looks promising. --Eric Begin forwarded message: > HeaderDoc 8 Public Beta is a tool for generating HTML reference > documentation from comments in C, C++, and Objective-C header files. > It's written in Perl for easy portability. Similar to JavaDoc, it > allows developers to easily document their interfaces and export > that information into HTML. HeaderDoc 8 adds many new features, > including a new (optional) tagless syntax, code coloring, > template-based index pages, improved error checking, man page > output, and support for many new languages, including Java, > JavaScript, Perl, PHP shell scripts, and Pascal. > http://developer.apple.com/darwin/projects/headerdoc

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5 DOF JoyStick/Mouse
by Steve 26 Jan '04

26 Jan '04

I have recently received a patent on a new mouse that also acts like a joystick. Could I get some feedback from your team? Are you in the business of developing prototypes? Please check this out and let me know what you think about it. Feel free to share the info with anyone that might be interested. Please follow the following link to view the details. http://www.elegantsol.com Thanks, Steve Stephen Shaw 8 Eiker Road Cranbury NJ 08512 H 609 799 4574 W 908 956 2266 Cell 609 284 0316

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Chimera dead after NVidia driver install...
by Patrick Ladam 12 Jan '04

12 Jan '04

Hi all, I had chimera 1.1872 working OK on my MDK 9.2 Linux box until I installed the NVidia driver for my GeFOrce2 card. What happens now is that chimera launches but stops during start-up with an error box indicating this message: "Togl: Couldn't get visual" This sounds like an OpenGL problem to me but I am far from being a specialist on this. Does anyone have a clue how I can debug/fix this ? Bye -- -- ----------------------------------------------------------------- | Patrick LADAM | | | Laboratoire CSSB | THE BIG BANG THEORY: | | UFR SMBH | | | 74 rue Marcel Cachin | In the begining there was | | 93017 Bobigny CEDEX | nothing at all. | | e-mail: | | | ladam(a)smbh.smbh.univ-paris13.fr | Then, it exploded... | | Tel: 01 48 38 77 26 / 76 85 | | | Fax: 01 48 38 77 77 | | -----------------------------------------------------------------

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python 2.3
by Catherine.Lozupone＠colorado.edu 06 Jan '04

06 Jan '04

Hello, I was wondering when Chimera will be using python 2.3 and how one would go about integrating the current version of Chimera with python 2.3. Thanks, Cathy Lozupone

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Re: [chimera-dev] Problem using: "openModels.add"
by Lars Kunert 07 Dec '03

07 Dec '03

Hi! How do I set the transformation matrix by hand? (and how do I get it? ) >So until we get the next snapshot release out (should be soon), you >will need to specify shareXform=0 and set the transformation matrix "by >hand" if you need to. Thanks for your help, Lars

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Problem using: "openModels.add"
by Lars Kunert 04 Dec '03

04 Dec '03

Hi! I got a problem using openModel.add to add a model into a specified id/subid-slot. Python 2.2.3 (#1, Oct 29 2003, 07:35:58) [GCC 3.2 20020903 (Red Hat Linux 8.0 3.2-7)] on linux2 Type "copyright", "credits" or "license" for more information. IDLE 0.8 -- press F1 for help >>> import chimera >>> m=chimera.Molecule() >>> chimera.openModels.add([m], baseId=0, subid=0 ) up till here it worked nicely... >>> m=chimera.Molecule() >>> chimera.openModels.add([m], baseId=0, subid=1 ) Traceback (most recent call last): File "<pyshell#4>", line 1, in ? chimera.openModels.add([m], baseId=0, subid=1 ) File "/usr/local/chimera/chimera-1.1872/share/chimera/__init__.py", line 769, in add shareXform, hidden, skipViewAll) error: unopen model adding a second, third... molecule/model to a slot gives an error-message (see above) - no new entry will show up in the model-viewer, but... >>> m=chimera.Molecule() the next created Model will be shown in the model-viewer without even being added. It would be nice if you could tell me something about the shareXform-parameter of the add-command too. Thanks a lot for your help, Lars

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Adding a button to my extension...
by Lars Kunert 24 Nov '03

24 Nov '03

Hi! My application (extension) works fine when execute it within the built-in IDLE. The python-code basically executes an external program (using "popen" ) and manages communication between the application and chimera through named pipes... (The external Application uses Qt and all my trials to smoothly integrate it by use of a python wrapper have failed...) Now I want to add an icon to chimera, which should call my extension in the same way I do it in the IDLE. I did not manage to get the ToolbarButtonPackage working: the related documentation seems to be completely outdated: ""The example code files and ToolbarButton.tiff must be saved in a directory named ToolbarButtonExtension. To run the example, start chimera, bring up the extension manager (via the Manager... entry in the Extensions menu), select the Directory tab, and Add the directory above the ToolbarButtonExtension directory. A MainChain entry should appear under the Utilities extension category."" Anyway, the ToolbarButtonExample works, but I can not adapt it to my application. When I add the path within the Favorites/Preferences/Tool - Tab chimera dies... I include the set of python files I use: Thanks for your help, Lars

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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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