December 2009 - Chimera-dev - RBVI Mailing Lists

Re: [chimera-dev] [Chimera-users] Programmer's Guide feedback....
by Eric Pettersen 15 Dec '09

15 Dec '09

On Dec 15, 2009, at 9:36 AM, Tom Goddard wrote: > 4. The ToolbarButton.py doesn't work unless the "import re" and > "import chimera" are in the function body. This is because Chimera > deletes all globals after loading a file. This has often been a > headache for me and Chimera should not delete globals. This is a behavior of Python. We load scripts into their own temporary module to avoid pollution of the Chimera main namespace (e.g. if the script defined globals named "id" or "sum" or "type" they would override built-in functions of the same name for all future script executions!). When Chimera unloads the temporary module, Python nulls out it's global namespace (to give garbage collection a shot at working). Now perhaps Chimera shouldn't unload the module. I think this would be a reasonable change. Perhaps it could be discussed at our next internal Chimera developers' meeting to ensure that I'm not forgetting any other ramifications that the change might have. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

2 2

odd plugin crash
by Mark Moll 09 Dec '09

09 Dec '09

I have a plugin for Chimera that uses its own binary python module. The module is statically linked against the system python2.5 library on Snow Leopard. When I select my plugin, Chimera crashes. Attached is the crash report with Chimera 1.4 (it happens with build 28940 and probably other versions as well). However, if I open Chimera from the command line like so: open /Users/mmoll/Downloads/Chimera.app then there is no crash. The module is linked against the following libraries: otool -L ~/labelhash/scripts/LabelHash/plat_darwin/_LabelHash.so /Users/mmoll/labelhash/scripts/LabelHash/plat_darwin/_LabelHash.so: /System/Library/Frameworks/Python.framework/Versions/2.5/Python (compatibility version 2.5.0, current version 2.5.1) /usr//lib/libmpi_cxx.0.dylib (compatibility version 1.0.0, current version 1.0.0) /usr//lib/libmpi.0.dylib (compatibility version 1.0.0, current version 1.0.0) /usr//lib/libopen-rte.0.dylib (compatibility version 1.0.0, current version 1.0.0) /usr//lib/libopen-pal.0.dylib (compatibility version 1.0.0, current version 1.0.0) /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib (compatibility version 1.0.0, current version 242.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.4.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4) I can also use this module without problems if I import it in a script that uses /usr/bin/python2.5. Is there some environment variable that could explain the different behaviors? -- Mark Process: python2.5 [18782] Path: /Users/mmoll/Downloads/Chimera.app/Contents/Resources/bin/python2.5 Identifier: edu.ucsf.cgl.chimera Version: 1.4.0 (1.4.0.29530) Code Type: X86 (Native) Parent Process: launchd [99] Date/Time: 2009-12-08 22:37:45.424 -0600 OS Version: Mac OS X 10.6.2 (10C540) Report Version: 6 Interval Since Last Report: 134941 sec Crashes Since Last Report: 5 Per-App Interval Since Last Report: 45 sec Per-App Crashes Since Last Report: 2 Anonymous UUID: F46D9EAC-0238-44B8-87A2-7475B19DB90E Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Crashed Thread: 0 Dispatch queue: com.apple.main-thread Application Specific Information: abort() called Thread 0 Crashed: Dispatch queue: com.apple.main-thread 0 libSystem.B.dylib 0x90799732 __kill + 10 1 libSystem.B.dylib 0x90799724 kill$UNIX2003 + 32 2 libSystem.B.dylib 0x9082c98d raise + 26 3 libSystem.B.dylib 0x908429d9 __abort + 124 4 libSystem.B.dylib 0x90842a55 abort_report_np + 0 5 libstdc++.6.dylib 0x94c05fda __gnu_cxx::__verbose_terminate_handler() + 433 6 libstdc++.6.dylib 0x94c0417a __cxxabiv1::__terminate(void (*)()) + 10 7 libstdc++.6.dylib 0x94c041ba __cxxabiv1::__unexpected(void (*)()) + 0 8 libstdc++.6.dylib 0x94c042b8 __gxx_exception_cleanup(_Unwind_Reason_Code, _Unwind_Exception*) + 0 9 libstdc++.6.dylib 0x94bc0856 std::__throw_logic_error(char const*) + 158 10 libstdc++.6.dylib 0x94bebced char* std::string::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag) + 57 11 libstdc++.6.dylib 0x94bec1fb std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&) + 53 12 _LabelHash.so 0x1a00fae4 __static_initialization_and_destruction_0(int, int) + 180 13 dyld 0x8fe0ed6d ImageLoaderMachO::doModInitFunctions(ImageLoader::LinkContext const&) + 235 14 dyld 0x8fe0d31e ImageLoader::recursiveInitialization(ImageLoader::LinkContext const&, unsigned int) + 246 15 dyld 0x8fe0d3d1 ImageLoader::runInitializers(ImageLoader::LinkContext const&) + 61 16 dyld 0x8fe0200b dyld::runInitializers(ImageLoader*) + 34 17 dyld 0x8fe0b299 dlopen + 558 18 libSystem.B.dylib 0x9073f048 dlopen + 66 19 org.python.python 0x000c6b7a _PyImport_GetDynLoadFunc + 283 (dynload_shlib.c:130) 20 org.python.python 0x000b4ed5 _PyImport_LoadDynamicModule + 107 (importdl.c:42) 21 org.python.python 0x000b2be5 load_module + 201 (import.c:1758) 22 org.python.python 0x000b30af import_submodule + 293 (import.c:2400) 23 org.python.python 0x000b32fd load_next + 195 (import.c:2220) 24 org.python.python 0x000b37aa import_module_level + 142 (import.c:2001) 25 org.python.python 0x000b3ca1 PyImport_ImportModuleLevel + 45 (import.c:2072) 26 org.python.python 0x0008eab3 builtin___import__ + 156 (bltinmodule.c:49) 27 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861) 28 org.python.python 0x0009389a PyEval_CallObjectWithKeywords + 112 (ceval.c:3442) 29 org.python.python 0x00096882 PyEval_EvalFrameEx + 8542 (ceval.c:2067) 30 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836) 31 org.python.python 0x0009b15e PyEval_EvalCode + 87 (ceval.c:500) 32 org.python.python 0x000b1fd2 PyImport_ExecCodeModuleEx + 193 (import.c:675) 33 org.python.python 0x000b2428 load_source_module + 726 (import.c:959) 34 org.python.python 0x000b2f07 load_package + 427 (import.c:1015) 35 org.python.python 0x000b30af import_submodule + 293 (import.c:2400) 36 org.python.python 0x000b32fd load_next + 195 (import.c:2220) 37 org.python.python 0x000b37aa import_module_level + 142 (import.c:2001) 38 org.python.python 0x000b3ca1 PyImport_ImportModuleLevel + 45 (import.c:2072) 39 org.python.python 0x0008eab3 builtin___import__ + 156 (bltinmodule.c:49) 40 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861) 41 org.python.python 0x0009389a PyEval_CallObjectWithKeywords + 112 (ceval.c:3442) 42 org.python.python 0x00096882 PyEval_EvalFrameEx + 8542 (ceval.c:2067) 43 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836) 44 org.python.python 0x0009b15e PyEval_EvalCode + 87 (ceval.c:500) 45 org.python.python 0x000b1fd2 PyImport_ExecCodeModuleEx + 193 (import.c:675) 46 org.python.python 0x000b2428 load_source_module + 726 (import.c:959) 47 org.python.python 0x000b2f07 load_package + 427 (import.c:1015) 48 org.python.python 0x000b30af import_submodule + 293 (import.c:2400) 49 org.python.python 0x000b32fd load_next + 195 (import.c:2220) 50 org.python.python 0x000b37aa import_module_level + 142 (import.c:2001) 51 org.python.python 0x000b3ca1 PyImport_ImportModuleLevel + 45 (import.c:2072) 52 org.python.python 0x0008eab3 builtin___import__ + 156 (bltinmodule.c:49) 53 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861) 54 org.python.python 0x0009389a PyEval_CallObjectWithKeywords + 112 (ceval.c:3442) 55 org.python.python 0x00096882 PyEval_EvalFrameEx + 8542 (ceval.c:2067) 56 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836) 57 org.python.python 0x0009b15e PyEval_EvalCode + 87 (ceval.c:500) 58 org.python.python 0x000b1fd2 PyImport_ExecCodeModuleEx + 193 (import.c:675) 59 org.python.python 0x000b2428 load_source_module + 726 (import.c:959) 60 org.python.python 0x000b30af import_submodule + 293 (import.c:2400) 61 org.python.python 0x000b32fd load_next + 195 (import.c:2220) 62 org.python.python 0x000b37aa import_module_level + 142 (import.c:2001) 63 org.python.python 0x000b3ca1 PyImport_ImportModuleLevel + 45 (import.c:2072) 64 org.python.python 0x0008eab3 builtin___import__ + 156 (bltinmodule.c:49) 65 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861) 66 org.python.python 0x0009389a PyEval_CallObjectWithKeywords + 112 (ceval.c:3442) 67 org.python.python 0x00096882 PyEval_EvalFrameEx + 8542 (ceval.c:2067) 68 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836) 69 org.python.python 0x0009b15e PyEval_EvalCode + 87 (ceval.c:500) 70 org.python.python 0x000b1fd2 PyImport_ExecCodeModuleEx + 193 (import.c:675) 71 org.python.python 0x000b2428 load_source_module + 726 (import.c:959) 72 org.python.python 0x000b30af import_submodule + 293 (import.c:2400) 73 org.python.python 0x000b32fd load_next + 195 (import.c:2220) 74 org.python.python 0x000b37aa import_module_level + 142 (import.c:2001) 75 org.python.python 0x000b3ca1 PyImport_ImportModuleLevel + 45 (import.c:2072) 76 org.python.python 0x0008eab3 builtin___import__ + 156 (bltinmodule.c:49) 77 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861) 78 org.python.python 0x0009389a PyEval_CallObjectWithKeywords + 112 (ceval.c:3442) 79 org.python.python 0x00096882 PyEval_EvalFrameEx + 8542 (ceval.c:2067) 80 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836) 81 org.python.python 0x0009b15e PyEval_EvalCode + 87 (ceval.c:500) 82 org.python.python 0x000b1fd2 PyImport_ExecCodeModuleEx + 193 (import.c:675) 83 org.python.python 0x000b2428 load_source_module + 726 (import.c:959) 84 org.python.python 0x000b2f07 load_package + 427 (import.c:1015) 85 org.python.python 0x000b30af import_submodule + 293 (import.c:2400) 86 org.python.python 0x000b32fd load_next + 195 (import.c:2220) 87 org.python.python 0x000b37aa import_module_level + 142 (import.c:2001) 88 org.python.python 0x000b3ca1 PyImport_ImportModuleLevel + 45 (import.c:2072) 89 org.python.python 0x0008eab3 builtin___import__ + 156 (bltinmodule.c:49) 90 org.python.python 0x0009a72f PyEval_EvalFrameEx + 24587 (ceval.c:3573) 91 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836) 92 org.python.python 0x000987b4 PyEval_EvalFrameEx + 16528 (ceval.c:3669) 93 org.python.python 0x00099b6a PyEval_EvalFrameEx + 21574 (ceval.c:3659) 94 org.python.python 0x00099b6a PyEval_EvalFrameEx + 21574 (ceval.c:3659) 95 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836) 96 org.python.python 0x00030007 function_call + 320 (funcobject.c:517) 97 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861) 98 org.python.python 0x0009389a PyEval_CallObjectWithKeywords + 112 (ceval.c:3442) 99 org.python.python 0x0008ed44 builtin_apply + 201 (bltinmodule.c:169) 100 org.python.python 0x0009a72f PyEval_EvalFrameEx + 24587 (ceval.c:3573) 101 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836) 102 org.python.python 0x00030007 function_call + 320 (funcobject.c:517) 103 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861) 104 org.python.python 0x00016946 instancemethod_call + 401 (classobject.c:2519) 105 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861) 106 org.python.python 0x0009389a PyEval_CallObjectWithKeywords + 112 (ceval.c:3442) 107 _tkinter.so 0x007dae57 PythonCmd + 220 (_tkinter.c:2014) 108 com.tcltk.tcllibrary 0x0185d0f7 TclInvokeStringCommand + 101 109 com.tcltk.tcllibrary 0x0185f67a Tcl_ListMathFuncs + 1281 110 com.tcltk.tcllibrary 0x0189c1e2 TclStackAlloc + 4767 111 com.tcltk.tcllibrary 0x018a4dc8 TclStackAlloc + 40581 112 com.tcltk.tcllibrary 0x018629df TclEvalObjEx + 788 113 com.tcltk.tcllibrary 0x01862ae1 Tcl_EvalObjEx + 47 114 com.tcltk.tklibrary 0x01961263 Tk_UndefineCursor + 234 115 com.tcltk.tklibrary 0x01962416 Tk_UndefineCursor + 4765 116 com.tcltk.tcllibrary 0x0185f67a Tcl_ListMathFuncs + 1281 117 com.tcltk.tcllibrary 0x0185fb77 Tcl_EvalObjv + 72 118 com.tcltk.tcllibrary 0x018627ce TclEvalObjEx + 259 119 com.tcltk.tcllibrary 0x018d9e62 TclObjGetFrame + 731 120 com.tcltk.tcllibrary 0x0185f67a Tcl_ListMathFuncs + 1281 121 com.tcltk.tcllibrary 0x0189c1e2 TclStackAlloc + 4767 122 com.tcltk.tcllibrary 0x018db5d3 TclObjInterpProcCore + 981 123 com.tcltk.tcllibrary 0x0185f67a Tcl_ListMathFuncs + 1281 124 com.tcltk.tcllibrary 0x01862102 Tcl_GetVersion + 6630 125 com.tcltk.tcllibrary 0x0186247a Tcl_EvalEx + 46 126 com.tcltk.tklibrary 0x01938e2a Tk_BindEvent + 4440 127 com.tcltk.tklibrary 0x0193da48 TkBindEventProc + 329 128 com.tcltk.tklibrary 0x01945969 Tk_HandleEvent + 1562 129 com.tcltk.tklibrary 0x01945a55 Tk_HandleEvent + 1798 130 com.tcltk.tcllibrary 0x018cc665 Tcl_ServiceEvent + 163 131 com.tcltk.tcllibrary 0x018cc977 Tcl_DoOneEvent + 365 132 _tkinter.so 0x007da74b Tkapp_MainLoop + 408 (_tkinter.c:2547) 133 org.python.python 0x0009a72f PyEval_EvalFrameEx + 24587 (ceval.c:3573) 134 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836) 135 org.python.python 0x000987b4 PyEval_EvalFrameEx + 16528 (ceval.c:3669) 136 org.python.python 0x00099b6a PyEval_EvalFrameEx + 21574 (ceval.c:3659) 137 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836) 138 org.python.python 0x000987b4 PyEval_EvalFrameEx + 16528 (ceval.c:3669) 139 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836) 140 org.python.python 0x0009b15e PyEval_EvalCode + 87 (ceval.c:500) 141 org.python.python 0x000be50c PyRun_FileExFlags + 260 (pythonrun.c:1273) 142 org.python.python 0x000be8a6 PyRun_SimpleFileExFlags + 640 (pythonrun.c:879) 143 org.python.python 0x000cbfce Py_Main + 3077 (main.c:523) 144 python2.5 0x000018ee _start + 216 145 python2.5 0x00001815 start + 41 Thread 1: Dispatch queue: com.apple.libdispatch-manager 0 libSystem.B.dylib 0x9075f0ea kevent + 10 1 libSystem.B.dylib 0x9075f804 _dispatch_mgr_invoke + 215 2 libSystem.B.dylib 0x9075ecc3 _dispatch_queue_invoke + 163 3 libSystem.B.dylib 0x9075ea68 _dispatch_worker_thread2 + 234 4 libSystem.B.dylib 0x9075e4f1 _pthread_wqthread + 390 5 libSystem.B.dylib 0x9075e336 start_wqthread + 30 Thread 2: 0 libSystem.B.dylib 0x9075e182 __workq_kernreturn + 10 1 libSystem.B.dylib 0x9075e718 _pthread_wqthread + 941 2 libSystem.B.dylib 0x9075e336 start_wqthread + 30 Thread 3: 0 libSystem.B.dylib 0x90774066 select$DARWIN_EXTSN$NOCANCEL + 10 1 libSystem.B.dylib 0x9080d11b select + 92 2 com.tcltk.tcllibrary 0x01900e76 TclUnixWaitForFile + 1347 3 libSystem.B.dylib 0x90765fbd _pthread_start + 345 4 libSystem.B.dylib 0x90765e42 thread_start + 34 Thread 4: 0 libSystem.B.dylib 0x907388da mach_msg_trap + 10 1 libSystem.B.dylib 0x90739047 mach_msg + 68 2 com.apple.opengl 0x912f2edb glcDebugListener + 426 3 libSystem.B.dylib 0x90765fbd _pthread_start + 345 4 libSystem.B.dylib 0x90765e42 thread_start + 34 Thread 0 crashed with X86 Thread State (32-bit): eax: 0x00000000 ebx: 0x90842969 ecx: 0xbfff40bc edx: 0x90799732 edi: 0xa0045b10 esi: 0x01c97f7c ebp: 0xbfff40d8 esp: 0xbfff40bc ss: 0x0000001f efl: 0x00000286 eip: 0x90799732 cs: 0x00000007 ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 cr2: 0x42789000 Binary Images: 0x1000 - 0x1fff +python2.5 ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/bin/python2.5 0x5000 - 0xf7fff +org.python.python 2.5a0 (2.5) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/Python 0x48c000 - 0x48cffd +_chimera.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/_chimera.so 0x490000 - 0x49a92f +libgfxinfo.dylib ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/libgfxinfo.dylib 0x4a3000 - 0x4a5e77 +libwrappy2.dylib ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/libwrappy2.dylib 0x4aa000 - 0x4ac267 +libtr.dylib ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/libtr.dylib 0x4b0000 - 0x4d8fd6 +libftgl.dylib ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/libftgl.dylib 0x4f9000 - 0x4f9ffd +libgfxinfo.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/libgfxinfo.so 0x600000 - 0x68360b +libotf.dylib ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/libotf.dylib 0x6a6000 - 0x6bba6b +libz.dylib ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/libz.dylib 0x712000 - 0x754fcf +_vrml.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/_vrml.so 0x787000 - 0x78afff +strop.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/strop.so 0x7d7000 - 0x7ddfff +_tkinter.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_tkinter.so 0x1000000 - 0x11fae17 +_chimera.dylib ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/_chimera.dylib 0x136a000 - 0x13cefeb +libfreetype.6.dylib ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/libfreetype.6.dylib 0x158d000 - 0x15bdfec +_surface.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/_surface.so 0x15ed000 - 0x15eeffd +MacOS.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/MacOS.so 0x15f7000 - 0x15f8ffb +math.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/math.so 0x1700000 - 0x17589df +librcarray.dylib ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/librcarray.dylib 0x1851000 - 0x191637f +com.tcltk.tcllibrary 8.5.7 (8.5.7) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Tcl.framework/Versions/8.5/Tcl 0x1933000 - 0x1a22daf +com.tcltk.tklibrary 8.5.7 (8.5.7) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Tk.framework/Versions/8.5/Tk 0x1a97000 - 0x1a99fff +operator.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/operator.so 0x1ae4000 - 0x1ae8ffb +_dotblas.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/_dotblas.so 0x1af4000 - 0x1af5fff +cStringIO.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/cStringIO.so 0x1d00000 - 0x1d66ff3 +multiarray.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/multiarray.so 0x1e6a000 - 0x1e99fe7 +umath.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/umath.so 0x1f1c000 - 0x1f30fff +_sort.so ??? 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(???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/gestalt.so 0x2800000 - 0x2818ffb +scalarmath.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/scalarmath.so 0x289c000 - 0x28a1fff +lapack_lite.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/linalg/lapack_lite.so 0x28ae000 - 0x28b6fef +fftpack_lite.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/fft/fftpack_lite.so 0x28c5000 - 0x28f3fff +mtrand.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/random/mtrand.so 0x294a000 - 0x2959ffb +_ctypes.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_ctypes.so 0x298f000 - 0x2992ffb +_struct.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_struct.so 0x2a20000 - 0x2a20fff +_weakref.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_weakref.so 0x2a66000 - 0x2a68fff +binascii.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/binascii.so 0x2a73000 - 0x2a74ff3 +_random.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_random.so 0x2a7c000 - 0x2a7dfff +fcntl.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/fcntl.so 0x12cb5000 - 0x12cc3fe7 libSimplifiedChineseConverter.dylib ??? (???) <4C9CC2D9-2F13-4465-5447-2516FCD9255B> /System/Library/CoreServices/Encodings/libSimplifiedChineseConverter.dylib 0x12cc7000 - 0x12cd9ff7 libTraditionalChineseConverter.dylib ??? (???) <C4E0D62B-4D1A-8DAD-D10B-2C055AA0479C> /System/Library/CoreServices/Encodings/libTraditionalChineseConverter.dylib 0x17e88000 - 0x17eccfdb +_imaging.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/PIL/_imaging.so 0x17f5f000 - 0x17f63fff +array.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/array.so 0x17fb4000 - 0x17fb4fff +_imagingtk.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/PIL/_imagingtk.so 0x185b9000 - 0x185bfffb +_socket.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_socket.so 0x185d5000 - 0x185d6ffb +_ssl.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_ssl.so 0x185e5000 - 0x1860bfff libssl.0.9.7.dylib ??? (???) <8BF98B2F-0F55-40CA-C082-43C76707BD24> /usr/lib/libssl.0.9.7.dylib 0x1861a000 - 0x186cffe7 libcrypto.0.9.7.dylib ??? (???) <4917E4F2-817F-5AC4-3FBE-54BC96360448> /usr/lib/libcrypto.0.9.7.dylib 0x187d5000 - 0x187d6ffb +select.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/select.so 0x187de000 - 0x187e0fff +collections.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/collections.so 0x187ed000 - 0x187f4757 +libTogl2.1.dylib ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/Togl2.1/libTogl2.1.dylib 0x18ac1000 - 0x18aeefff +libTix8.4.3.dylib ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/Tix8.4.3/libTix8.4.3.dylib 0x18afe000 - 0x18c6fff7 GLEngine ??? (???) <D336658A-F6DB-6D61-9CA6-04299E7D5420> /System/Library/Frameworks/OpenGL.framework/Resources/GLEngine.bundle/GLEngine 0x18ca0000 - 0x18edcfef com.apple.ATIRadeonX1000GLDriver 1.6.6 (6.0.6) <E0A5525E-5037-2D4A-0879-2FB8F865FBC2> /System/Library/Extensions/ATIRadeonX1000GLDriver.bundle/Contents/MacOS/ATIRadeonX1000GLDriver 0x18eff000 - 0x18f1bff7 GLRendererFloat ??? (???) <8FF7B576-512C-C2F8-4C0C-967FB3D9EEA2> /System/Library/Frameworks/OpenGL.framework/Resources/GLRendererFloat.bundle/GLRendererFloat 0x19015000 - 0x19023ffc +x509.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/x509.so 0x19031000 - 0x19032fff +icglue.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/icglue.so 0x190fe000 - 0x19101fff +_AE.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_AE.so 0x1910e000 - 0x1910ffff +_Evt.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_Evt.so 0x19117000 - 0x1911dfff +_File.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_File.so 0x193ba000 - 0x193c1ff7 mca_ns_proxy.so ??? (???) <62A3719D-F257-B6E0-86CC-64BBD8B207CA> /usr/lib/openmpi/mca_ns_proxy.so 0x193c6000 - 0x193c6ff7 mca_errmgr_hnp.so ??? (???) <3DCE56BF-2B74-B2C6-08A1-851FC9E536F2> /usr/lib/openmpi/mca_errmgr_hnp.so 0x194f8000 - 0x19503fef +datetime.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/datetime.so 0x19526000 - 0x19529fff +_Res.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_Res.so 0x19738000 - 0x19746ffb libmpi_cxx.0.dylib ??? (???) <FC254088-F371-1442-3057-AD266C9FC0D6> /usr/lib/libmpi_cxx.0.dylib 0x1975c000 - 0x197a0ff7 libopen-rte.0.dylib ??? (???) <3F16BADE-3E33-E81A-1351-27AB5D5A084A> /usr/lib/libopen-rte.0.dylib 0x197b4000 - 0x197b9ff7 mca_ns_replica.so ??? (???) <B54408AC-EB76-5D46-69EB-7544AFA7AD14> /usr/lib/openmpi/mca_ns_replica.so 0x197be000 - 0x197beff7 mca_errmgr_orted.so ??? (???) <D2E4861C-5F83-E02B-87BE-790F388B0B6A> /usr/lib/openmpi/mca_errmgr_orted.so 0x197c2000 - 0x197c3ff7 mca_errmgr_proxy.so ??? (???) <2D7C420C-B47C-DE84-0853-813F8781362B> /usr/lib/openmpi/mca_errmgr_proxy.so 0x197c7000 - 0x197c7ff7 mca_rml_oob.so ??? (???) <DC93F712-FCC6-5051-EE82-4DD21D720DFA> /usr/lib/openmpi/mca_rml_oob.so 0x197cb000 - 0x197d8ff7 mca_oob_tcp.so ??? (???) <B3F70BE5-BDAD-4868-ACFE-5FF01973311D> /usr/lib/openmpi/mca_oob_tcp.so 0x197de000 - 0x197e6ff7 mca_gpr_proxy.so ??? (???) <3BC17D82-54FE-8912-BEA8-22F05549ED04> /usr/lib/openmpi/mca_gpr_proxy.so 0x197ec000 - 0x197f0ff7 mca_rds_hostfile.so ??? (???) <7D239E39-7E10-5E1F-5FBC-1D9ED0A9BAF1> /usr/lib/openmpi/mca_rds_hostfile.so 0x197f5000 - 0x197f5ff7 mca_rds_proxy.so ??? (???) <5E48AB54-1685-F0B7-2B06-27C168B211B4> /usr/lib/openmpi/mca_rds_proxy.so 0x197f9000 - 0x197fbff7 mca_rds_resfile.so ??? (???) <5F8A007F-4C83-E733-84E1-AAA2B48F0778> /usr/lib/openmpi/mca_rds_resfile.so 0x1a000000 - 0x1a64fff7 +_LabelHash.so ??? (???) <C8C3D70D-4280-3793-D3CB-D687C21C03AD> /Users/mmoll/labelhash/ViewMatch/LabelHash/plat_darwin/_LabelHash.so 0x1abe5000 - 0x1ac67ff7 libmpi.0.dylib ??? (???) <16F27F3C-476D-8369-AE4C-32F5F2A926F4> /usr/lib/libmpi.0.dylib 0x1ac8f000 - 0x1acb5ff7 libopen-pal.0.dylib ??? (???) <A0AE0C02-73AA-AB1E-234C-C86A56258BF9> /usr/lib/libopen-pal.0.dylib 0x1ace3000 - 0x1acfaff7 mca_gpr_replica.so ??? (???) <11983E61-BE75-7DD8-D86D-3F2265B1E3B5> /usr/lib/openmpi/mca_gpr_replica.so 0x1ad02000 - 0x1ad02ff7 mca_ras_dash_host.so ??? (???) <04CEEC4D-29FE-1069-BE82-FCFE4D57EDD6> /usr/lib/openmpi/mca_ras_dash_host.so 0x1ad06000 - 0x1ad07ff7 mca_ras_gridengine.so ??? (???) <D3852780-27C3-41E3-65FE-7F77E37F996C> /usr/lib/openmpi/mca_ras_gridengine.so 0x1ad0b000 - 0x1ad0bff7 mca_ras_localhost.so ??? (???) <EB8A4059-3163-8878-B10D-7EEC83084D51> /usr/lib/openmpi/mca_ras_localhost.so 0x1ad0f000 - 0x1ad0fff7 mca_ras_xgrid.so ??? (???) <22885FDF-D27A-C329-5D0C-C22E8886FF80> /usr/lib/openmpi/mca_ras_xgrid.so 0x1ad13000 - 0x1ad14ff7 mca_rmaps_round_robin.so ??? (???) <75E4C219-8493-F1DB-2330-3E5AD57ECF8B> /usr/lib/openmpi/mca_rmaps_round_robin.so 0x1ad18000 - 0x1ad1aff7 mca_pls_gridengine.so ??? (???) <475CC77C-F249-0831-34C9-8B73D7729036> /usr/lib/openmpi/mca_pls_gridengine.so 0x1ad1f000 - 0x1ad21ff7 mca_pls_proxy.so ??? (???) <F2D3DDFE-07CE-9741-6ECC-22E42ABA5428> /usr/lib/openmpi/mca_pls_proxy.so 0x1ad25000 - 0x1ad29ff7 mca_pls_rsh.so ??? (???) <61F2DBD1-B245-34FC-474E-8FC73DD1A023> /usr/lib/openmpi/mca_pls_rsh.so 0x1ad2e000 - 0x1ad32ff7 mca_pls_xgrid.so ??? (???) <23F68E3D-3C8E-A386-2D43-37EBCADABC67> /usr/lib/openmpi/mca_pls_xgrid.so 0x1ad38000 - 0x1ad9bfe7 com.apple.xgrid.foundation 10.6 (94.1) <2EAE7136-AAA5-CD23-BB46-055BF1E1E73E> /System/Library/Frameworks/XgridFoundation.framework/Versions/A/XgridFoundation 0x1addf000 - 0x1ae04fe7 com.apple.xgrid.beep 10.6 (94.1) <8E80558B-4395-96A9-D359-C31906A989A3> /System/Library/PrivateFrameworks/BEEP.framework/Versions/A/BEEP 0x1ae21000 - 0x1ae5efe7 com.apple.frameworks.server.foundation 10.6.2 (93.2) <1A6015EC-F367-E3EB-C09C-A14D495DF548> /System/Library/PrivateFrameworks/ServerFoundation.framework/Versions/A/ServerFoundation 0x1ae83000 - 0x1ae94ff7 com.apple.PlatformHardwareManagement 2.0.1 (2.0.1) <6F51F043-35B8-42FE-B37C-229304A963CC> /System/Library/PrivateFrameworks/PlatformHardwareManagement.framework/Versions/A/PlatformHardwareManagement 0x1aea0000 - 0x1aed5ff7 com.apple.coreWLAN.framework 6.1 (610.2) <076D9FD8-D3AB-C9A9-E388-13C6B132ECC3> /System/Library/Frameworks/CoreWLAN.framework/Versions/A/CoreWLAN 0x1aee9000 - 0x1aeedff7 mca_odls_default.so ??? (???) <0C23ECED-3E14-1716-9EE0-534C25E375AF> /usr/lib/openmpi/mca_odls_default.so 0x1aef2000 - 0x1aef3ff7 mca_rmgr_proxy.so ??? (???) <68ECDB74-4599-A95D-D426-296F99A52767> /usr/lib/openmpi/mca_rmgr_proxy.so 0x1aef7000 - 0x1aef8ff7 mca_rmgr_urm.so ??? (???) <665D7808-D33C-91F1-BD09-53B6B181FDE9> /usr/lib/openmpi/mca_rmgr_urm.so 0x1aefc000 - 0x1aefcff7 mca_allocator_basic.so ??? (???) <EC184B3B-DC11-0470-8CB8-8B003AF45BD6> /usr/lib/openmpi/mca_allocator_basic.so 0x1af01000 - 0x1af04ff7 mca_iof_svc.so ??? (???) <44069198-D8BE-06F4-F8EF-370629014A19> /usr/lib/openmpi/mca_iof_svc.so 0x1af09000 - 0x1af09ff7 mca_allocator_bucket.so ??? (???) <306037E5-69E6-7F4E-1075-F4970B7D8644> /usr/lib/openmpi/mca_allocator_bucket.so 0x1af0d000 - 0x1af0eff7 mca_rcache_vma.so ??? (???) <5B1F5B9B-D6D0-5813-14BF-7BCAF078D108> /usr/lib/openmpi/mca_rcache_vma.so 0x1af12000 - 0x1af13ff7 mca_mpool_rdma.so ??? (???) <E229B6FE-D53F-4268-750C-0768BEE4914D> /usr/lib/openmpi/mca_mpool_rdma.so 0x1af17000 - 0x1af18ff7 mca_mpool_sm.so ??? (???) <CF63D7E2-2213-B42C-A28C-B839941D8990> /usr/lib/openmpi/mca_mpool_sm.so 0x1af1c000 - 0x1af1cff7 libmca_common_sm.0.dylib ??? (???) <A9DAA464-4988-DC12-CDBB-71CED6B9E434> /usr/lib/libmca_common_sm.0.dylib 0x1af20000 - 0x1af2dff7 mca_pml_ob1.so ??? (???) <8ADBA0E2-BE0F-2A14-AA3F-09B7345F5E0C> /usr/lib/openmpi/mca_pml_ob1.so 0x1af33000 - 0x1af34ff7 mca_bml_r2.so ??? (???) <BBFC5ED1-BCE6-CB47-9EF0-69A2EA2FA1DA> /usr/lib/openmpi/mca_bml_r2.so 0x1af38000 - 0x1af3aff7 mca_btl_self.so ??? (???) <86CEE87A-2E2F-7145-1EBD-AB54031D98D9> /usr/lib/openmpi/mca_btl_self.so 0x1af3e000 - 0x1af41ff7 mca_btl_sm.so ??? (???) <E6F0C188-72DA-F83E-C60C-E2B5664CEA9B> /usr/lib/openmpi/mca_btl_sm.so 0x1af47000 - 0x1af4dff7 mca_btl_tcp.so ??? (???) <19B20969-02FE-A65A-2778-C302481B60D9> /usr/lib/openmpi/mca_btl_tcp.so 0x1af53000 - 0x1af58ff7 mca_coll_basic.so ??? (???) <BBE0D1BD-E2B8-0C84-DF96-1BD9399F42F3> /usr/lib/openmpi/mca_coll_basic.so 0x1af5d000 - 0x1af5dff7 mca_coll_self.so ??? (???) <8F84C5BA-8EF9-302E-CC60-97B0CE460579> /usr/lib/openmpi/mca_coll_self.so 0x1af61000 - 0x1af64ff7 mca_coll_sm.so ??? (???) <5181BF17-A287-100E-A3A7-CF6D3A09C4E0> /usr/lib/openmpi/mca_coll_sm.so 0x1af69000 - 0x1af75ff7 mca_coll_tuned.so ??? (???) <379F7169-FB92-48F3-0C86-54E53D50AEF1> /usr/lib/openmpi/mca_coll_tuned.so 0x1af7b000 - 0x1af82ff7 mca_osc_pt2pt.so ??? (???) <AE551799-E5D3-05B8-A046-187B1ACFA708> /usr/lib/openmpi/mca_osc_pt2pt.so 0x8fe00000 - 0x8fe4162b dyld 132.1 (???) <211AF0DD-42D9-79C8-BB6A-1F4BEEF4B4AB> /usr/lib/dyld 0x90029000 - 0x901a0fef com.apple.CoreFoundation 6.6.1 (550.13) <AE9FC6F7-F0B2-DE58-759E-7DB89C021A46> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 0x901b6000 - 0x90391ff3 libType1Scaler.dylib ??? 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(???) <D45B91B2-2B4C-AAC0-8096-1FC48B7E9672> /usr/lib/libSystem.B.dylib 0x908fb000 - 0x9095bfe7 com.apple.CoreText 3.1.0 (???) <79FD1B5C-2F93-4C5D-B07B-4DD9088E67DE> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreText.framework/Versions/A/CoreText 0x9097e000 - 0x90982ff7 libGFXShared.dylib ??? (???) <79F4F60E-0A6D-CE9C-282E-FA85825449E3> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib 0x90983000 - 0x90ca6fef com.apple.HIToolbox 1.6.2 (???) <E02640B9-7BC3-A4B4-6202-9E4127DDFDD6> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox 0x90ca7000 - 0x90cb5fe7 libz.1.dylib ??? (???) <7B7A02AB-DA99-6180-880E-D28E4F9AA8EB> /usr/lib/libz.1.dylib 0x90cb6000 - 0x90cebff7 libcups.2.dylib ??? (???) <BE4E095C-EECA-017E-11AA-C65F4D2B15C8> /usr/lib/libcups.2.dylib 0x90fe1000 - 0x90fecff7 libCSync.A.dylib ??? (???) <9292E6E3-70C1-1DD7-4213-1044F0FA8381> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCSync.A.dylib 0x90fed000 - 0x9125dffb com.apple.Foundation 6.6.1 (751.14) <CD815A50-BB33-5AA1-DD73-A5B07D394DDA> /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation 0x9125e000 - 0x91279ff7 libPng.dylib ??? (???) <3F8682CD-C05B-607D-96E7-767646C77DB8> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib 0x912b1000 - 0x912eeff7 com.apple.SystemConfiguration 1.10.1 (1.10.1) <BA676C76-6AAD-F630-626D-B9248535294D> /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration 0x912ef000 - 0x912fcff7 com.apple.opengl 1.6.5 (1.6.5) <0AE8B897-8A80-2C14-D6FC-DC21AC423234> /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL 0x912fd000 - 0x91302ff7 com.apple.OpenDirectory 10.6 (10.6) <92582807-E8F3-3DD9-EB42-4195CFB754A1> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/OpenDirectory 0x91303000 - 0x91305ff7 com.apple.securityhi 4.0 (36638) <962C66FB-5BE9-634E-0810-036CB340C059> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI 0x91306000 - 0x9139efe7 edu.mit.Kerberos 6.5.9 (6.5.9) <73EC847F-FF44-D542-2AD5-97F6C8D48F0B> /System/Library/Frameworks/Kerberos.framework/Versions/A/Kerberos 0x915d2000 - 0x91679fe7 com.apple.CFNetwork 454.5 (454.5) <A7E78E62-0C59-CE57-73D2-C4E60527781C> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/Versions/A/CFNetwork 0x9167a000 - 0x9167aff7 com.apple.Accelerate.vecLib 3.5 (vecLib 3.5) <3E039E14-2A15-56CC-0074-EE59F9FBB913> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib 0x9175b000 - 0x91767ff7 libkxld.dylib ??? (???) <3D2C5BA3-6A8D-C861-B346-0E19942D9AF1> /usr/lib/system/libkxld.dylib 0x91768000 - 0x91832fef com.apple.CoreServices.OSServices 352 (352) <D9F21CA4-EED0-705F-8F3C-F1322D114B52> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices 0x91833000 - 0x91934fe7 libxml2.2.dylib ??? (???) <B4C5CD68-405D-0F1B-59CA-5193D463D0EF> /usr/lib/libxml2.2.dylib 0x9194b000 - 0x9195cff7 com.apple.LangAnalysis 1.6.6 (1.6.6) <7A3862F7-3730-8F6E-A5DE-8E2CCEA979EF> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis 0x9195d000 - 0x91983fff com.apple.DictionaryServices 1.1.1 (1.1.1) <02709230-9B37-C743-6E27-3FCFD18211F8> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/DictionaryServices 0x91984000 - 0x919beffb libFontRegistry.dylib ??? (???) <72342297-E8D6-B071-A752-014134129282> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib 0x919bf000 - 0x91a19ff7 com.apple.framework.IOKit 2.0 (???) <1BE07087-27D5-0E62-F06B-007C2BED4073> /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit 0x91a1a000 - 0x91a4eff7 libssl.0.9.8.dylib ??? (???) <F3402001-EC8D-58E5-4A23-02A979C9E857> /usr/lib/libssl.0.9.8.dylib 0x91a50000 - 0x922334b7 com.apple.CoreGraphics 1.536.12 (???) <263EB5FC-DEAD-7C5B-C486-EC86C173F952> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics 0x92234000 - 0x92267ff7 com.apple.AE 496.1 (496.1) <1AC75AE2-AF94-2458-0B94-C3BB0115BA4B> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE 0x92328000 - 0x92328ff7 com.apple.Cocoa 6.6 (???) <EA27B428-5904-B00B-397A-185588698BCC> /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa 0x932d8000 - 0x93302ff7 com.apple.framework.Admin 4.0 (4.0) <4A434473-A6C1-3F40-2928-16CFF1222FA1> /System/Library/PrivateFrameworks/Admin.framework/Versions/A/Admin 0x93d4d000 - 0x93d9dfe7 libGLU.dylib ??? (???) <659ADCA2-10EC-59BD-1B0A-4928A965F1D1> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib 0x93df7000 - 0x93e94fe3 com.apple.LaunchServices 362 (362) <8BE1C1A1-BF71-CE07-F3FB-6057D47AF461> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices 0x94344000 - 0x94344ff7 liblangid.dylib ??? (???) <B99607FC-5646-32C8-2C16-AFB5EA9097C2> /usr/lib/liblangid.dylib 0x94381000 - 0x9438aff7 com.apple.DiskArbitration 2.3 (2.3) <E9C40767-DA6A-6CCB-8B00-2D5706753000> /System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration 0x9438b000 - 0x947c0ff7 libLAPACK.dylib ??? (???) <5E2D2283-57DE-9A49-1DB0-CD027FEFA6C2> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib 0x947c1000 - 0x947c4fe7 libmathCommon.A.dylib ??? (???) <1622A54F-1A98-2CBE-B6A4-2122981A500E> /usr/lib/system/libmathCommon.A.dylib 0x947c5000 - 0x94816ff7 com.apple.HIServices 1.8.0 (???) <B8EC13DB-A81A-91BF-8C82-66E840C64C91> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices 0x94886000 - 0x94890ff7 libGL.dylib ??? (???) <76A207FE-889A-CF1B-AF9A-795EEE5A463E> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib 0x94891000 - 0x94944fff libFontParser.dylib ??? (???) <FAD5E96D-CF93-CC86-6B30-A6594B930772> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib 0x94b28000 - 0x94bb9fe7 com.apple.print.framework.PrintCore 6.1 (312.3) <6D4322AF-703C-CC19-77B4-53E6D3BB18D4> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore 0x94bba000 - 0x94c24fe7 libstdc++.6.dylib ??? (???) <411D87F4-B7E1-44EB-F201-F8B4F9227213> /usr/lib/libstdc++.6.dylib 0x94e3e000 - 0x94ee6ffb com.apple.QD 3.33 (???) <196CDBA6-5B87-2767-DD57-082D71B0A5C7> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD 0x94f42000 - 0x94f42ff7 com.apple.ApplicationServices 38 (38) <8012B504-3D83-BFBB-DA65-065E061CFE03> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices 0x94fe4000 - 0x95064feb com.apple.SearchKit 1.3.0 (1.3.0) <9E18AEA5-F4B4-8BE5-EEA9-818FC4F46FD9> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/SearchKit 0x9508b000 - 0x9517dff7 libcrypto.0.9.8.dylib ??? (???) <792B8722-3091-5E9F-E25F-67499CFE0599> /usr/lib/libcrypto.0.9.8.dylib 0x9517e000 - 0x9518bff7 com.apple.NetFS 3.2.1 (3.2.1) <5E61A00B-FA16-9D99-A064-47BDC5BC9A2B> /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS 0x9518c000 - 0x9518dff7 com.apple.audio.units.AudioUnit 1.6.1 (1.6.1) <3A08510C-07F7-1A09-D6ED-1A488203ACCC> /System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit 0x9518e000 - 0x951d0fe7 libvDSP.dylib ??? (???) <8F8FFFB3-81E3-2969-5688-D5B0979182E6> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib 0x951d1000 - 0x952fdfe3 com.apple.audio.toolbox.AudioToolbox 1.6.1 (1.6.1) <C226DF5C-35B0-98B8-95ED-FE5FE24E62C8> /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox 0x952fe000 - 0x9530eff7 libsasl2.2.dylib ??? (???) <C8744EA3-0AB7-CD03-E639-C4F2B910BE5D> /usr/lib/libsasl2.2.dylib 0x9530f000 - 0x95405ff7 libGLProgrammability.dylib ??? (???) <82D03736-D30C-C013-BBB1-20ED9687D47F> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib 0x95406000 - 0x954e3ff7 com.apple.vImage 4.0 (4.0) <64597E4B-F144-DBB3-F428-0EC3D9A1219E> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage 0x954e7000 - 0x954fbfe7 libbsm.0.dylib ??? (???) <14CB053A-7C47-96DA-E415-0906BA1B78C9> /usr/lib/libbsm.0.dylib 0x95535000 - 0x95576ff7 libRIP.A.dylib ??? (???) <9F0ECE75-1F03-60E4-E29C-136A27C13F2E> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libRIP.A.dylib 0x95577000 - 0x95870fef com.apple.QuickTime 7.6.3 (1591.3) <803CC5FD-2369-83B5-795D-A8963620EFAC> /System/Library/Frameworks/QuickTime.framework/Versions/A/QuickTime 0x959f4000 - 0x95a16fef com.apple.DirectoryService.Framework 3.6 (621.1) <3ED4949F-9604-C109-6586-5CE5F421182B> /System/Library/Frameworks/DirectoryService.framework/Versions/A/DirectoryService 0x95a48000 - 0x95af7ff3 com.apple.ColorSync 4.6.2 (4.6.2) <F3F097AC-FDB7-3357-C64F-E28BECF4C15F> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync 0x95c03000 - 0x95c0dff7 com.apple.bsd.ServiceManagement 1.0 (1.0) <B007CBE8-2539-CC71-9675-9EC04196921F> /System/Library/Frameworks/ServiceManagement.framework/Versions/A/ServiceManagement 0x95e49000 - 0x95e49ff7 com.apple.CoreServices 44 (44) <AC35D112-5FB9-9C8C-6189-5F5945072375> /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices 0x95f16000 - 0x9632cff7 libBLAS.dylib ??? (???) <C4FB303A-DB4D-F9E8-181C-129585E59603> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 0x96354000 - 0x96366ff7 com.apple.MultitouchSupport.framework 204.9 (204.9) <B639F02B-33CC-150C-AE8C-1007EA7648F9> /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport 0x96593000 - 0x967f5ff7 com.apple.security 6.0 (36910) <32B8FA26-CD73-4C45-C15A-EF8406D51FCC> /System/Library/Frameworks/Security.framework/Versions/A/Security 0x967f6000 - 0x967f9ff7 libCGXType.A.dylib ??? (???) <483FCF1C-066B-D210-7355-ABC48CA9DB2F> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCGXType.A.dylib 0x96824000 - 0x9689efef com.apple.audio.CoreAudio 3.2.2 (3.2.2) <1F97B48A-327B-89CC-7C01-3865179716E0> /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio 0x9689f000 - 0x968a6fff com.apple.print.framework.Print 6.0 (237) <7A06B15C-B835-096E-7D96-C2FE8F0D21E1> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print 0x968aa000 - 0x96a66fef com.apple.ImageIO.framework 3.0.1 (3.0.1) <598CF4F9-7542-E1A7-26D2-584933497A2E> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO 0x96a67000 - 0x96dceff7 com.apple.QuartzCore 1.6.1 (227.8) <8B90AB08-46A4-1C5C-4E71-C6AB652477B9> /System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore 0x96e4a000 - 0x96e6afe7 libresolv.9.dylib ??? (???) <A48921CB-3FA7-3071-AF9C-2D86FB493A3A> /usr/lib/libresolv.9.dylib 0x96fda000 - 0x97023fe7 libTIFF.dylib ??? (???) <5864AE5B-EAEB-F8B6-18FB-3D27B7895A4C> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib 0x97024000 - 0x97027ff7 libCoreVMClient.dylib ??? (???) <A89D7A78-8FB0-2BDF-30DB-A35E04A6186B> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib 0x97028000 - 0x97075feb com.apple.DirectoryService.PasswordServerFramework 6.0 (6.0) <BF66BA5D-BBC8-78A5-DBE2-F9DE3DD1D775> /System/Library/PrivateFrameworks/PasswordServer.framework/Versions/A/PasswordServer 0x97089000 - 0x970cdfe7 com.apple.Metadata 10.6.2 (507.4) <DBCBAE7D-7B34-7806-C0B9-1E6E6D45562F> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata 0x970ce000 - 0x970eefe7 com.apple.opencl 12 (12) <2DB56F60-577B-6724-5708-7B082F62CC0F> /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL 0x970ef000 - 0x970fcff7 libbz2.1.0.dylib ??? (???) <495732E1-2AC4-44FC-E633-4CBCC503B924> /usr/lib/libbz2.1.0.dylib 0x972c6000 - 0x972c6ff7 com.apple.Carbon 150 (152) <608A04AB-F35D-D2EB-6629-16B88FB32074> /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon 0x97318000 - 0x9731cff7 libGIF.dylib ??? (???) <83FB0DCC-355F-A930-E570-0BD95086CC59> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib 0x9732b000 - 0x9733fffb com.apple.speech.synthesis.framework 3.10.35 (3.10.35) <57DD5458-4F24-DA7D-0927-C3321A65D743> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis 0x97340000 - 0x97343ffb com.apple.help 1.3.1 (41) <67F1F424-3983-7A2A-EC21-867BE838E90B> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Help.framework/Versions/A/Help 0x97344000 - 0x97360fe3 com.apple.openscripting 1.3.1 (???) <DA16DE48-59F4-C94B-EBE3-7FAF772211A2> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting 0x97446000 - 0x97477ff3 libTrueTypeScaler.dylib ??? 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(???) <A6007BF7-BF3C-96DC-C435-849C6B88C58A> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib 0x988ca000 - 0x988ccff7 libRadiance.dylib ??? (???) <462903E2-2E77-FAE5-4ED6-829AAB1980A4> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib 0x98a4d000 - 0x98ae9fe7 com.apple.ApplicationServices.ATS 4.1 (???) <EA26375D-8276-9671-645D-D28CAEC95292> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS 0x98aea000 - 0x98b12ff7 libxslt.1.dylib ??? 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implementing MMTK normal calculations in chimera
by Victor Muñoz 09 Dec '09

09 Dec '09

Dear developpers, I am trying to make an extension that allows normal mode calculations with MMTK into chimera. I have several problems beginning with the following. I have first used the MMTKinter.py and added a new function called NM_ffm that calculates normal modes with a full atom force field. This works perfectly (although I am not yet able to make an animation in chimera that follows the vectors calculated...that will be a future question for you). Then I added another function (NM_mcm) that allows me to do NM calculations with the mechanical constraint (see http://dirac.cnrs-orleans.fr/MMTK/using-mmtk/mmtk-example-scripts/normal-mo…). For this I need to define a subspace that requires a universe.protein object (the functions are given at the end of the mail). Unfortunately, I can not pass the molecular object from the chimera space as a universe.protein object. We thought in putting self.universe.protein call into the _makeUniverse function in MMTKinter.py but that did not work. We tried other combinations but we now face the fact that we are blocked. May be we need another function in order to define subspaces but yet we still don't know how to pass chimera infos to MMTK. Could you give me a hand so that I can define correctly subspaces on chimera molecules? All the best and thank in advance for any help, Victor ************* Computational Biotechnological Chemistry @transmet ####Function for normal modes calculations in full atom ff def NM_ffm(self, nsteps, stepsize=0.02, interval=None, action=None, **kw): from chimera import replyobj timestamp("_minimize") from MMTK import Units from MMTK.ForceFields.Amber import AmberData from MMTK.Minimization import SteepestDescentMinimizer from MMTK.Trajectory import LogOutput # from JD to make NM calculations from MMTK.NormalModes import NormalModes from chimera import runCommand as run from chimera import selection as sele from chimera import Point, Vector import os, sys # JD'end import sys if not interval: actions = [] else: actions = [ LogOutput(sys.stdout, ["energy"], interval, None, interval) ] kw["step_size"] = stepsize * Units.Ang minimizer = SteepestDescentMinimizer(self.universe, actions=actions, **kw) if action is None or not interval: interval = None msg = "Initial energy: %f" % self.universe.energy() replyobj.status(msg) replyobj.info(msg) saveNormalizeName = AmberData._normalizeName AmberData._normalizeName = simpleNormalizeName remaining = nsteps while remaining > 0: timestamp(" minimize interval") if interval is None: realSteps = remaining else: realSteps = min(remaining, interval) minimizer(steps=realSteps) remaining -= realSteps if action is not None: action(self) timestamp(" finished %d steps" % realSteps) msg = "Finished %d of %d minimization steps" % ( nsteps - remaining, nsteps) replyobj.status(msg) replyobj.info(msg) replyobj.info("\n") #Calculate normal modes JD's trucho def despl(vec): run("sel #0") atoms=sele.currentAtoms() for a in atoms: a.setCoord(a.xformCoord()-10*(vec)) modes = NormalModes(self.universe) for mode in modes: print mode print mode.array L1=[] L2=[] L3=[] for mode in modes: y=6 u=len(mode.array) while y<u: L1.append(mode.array[y][0]) L2.append(mode.array[y][1]) L3.append(mode.array[y][2]) y+=1 y=0 run("sel:all") atoms=sele.currentAtoms() run("~sel") u=len(L1) a=0 o=len(atoms) while y<u: vec=Vector(float(L1[y]),float(L2[y]),float(L3[y])) atoms[a].setCoord(atoms[a].coord()-(vec)) a+=1 if a==o: a=0 raw_input() else: pass y+=1 #JD's end return modes AmberData._normalizeName = saveNormalizeName timestamp("end _minimize") ####Function for mechanical constraint def NM_mcm(self, nsteps, stepsize=0.02, interval=None, action=None, **kw): from MMTK import * from MMTK.Proteins import Protein from MMTK.ForceFields import Amber94ForceField from MMTK.NormalModes import NormalModes, SubspaceNormalModes from MMTK.Subspace import RigidMotionSubspace from MMTK.Minimization import ConjugateGradientMinimizer from MMTK.Trajectory import StandardLogOutput import numpy # Victor Modifications from chimera import replyobj timestamp("_minimize") from MMTK import Units from MMTK.ForceFields.Amber import AmberData from MMTK.Minimization import SteepestDescentMinimizer from MMTK.Trajectory import LogOutput from MMTK.NormalModes import NormalModes from chimera import runCommand as run from chimera import selection as sele from chimera import Point, Vector import os, sys #/end if not interval: actions = [] else: actions = [ LogOutput(sys.stdout, ["energy"], interval, None, interval) ] kw["step_size"] = stepsize * Units.Ang minimizer = SteepestDescentMinimizer(self.universe, actions=actions, **kw) if action is None or not interval: interval = None msg = "Initial energy: %f" % self.universe.energy() replyobj.status(msg) replyobj.info(msg) saveNormalizeName = AmberData._normalizeName AmberData._normalizeName = simpleNormalizeName remaining = nsteps while remaining > 0: timestamp(" minimize interval") if interval is None: realSteps = remaining else: realSteps = min(remaining, interval) minimizer(steps=realSteps) remaining -= realSteps if action is not None: action(self) timestamp(" finished %d steps" % realSteps) msg = "Finished %d of %d minimization steps" % ( nsteps - remaining, nsteps) replyobj.status(msg) replyobj.info(msg) replyobj.info("\n") # Construct system #self.universe = InfiniteUniverse(Amber94ForceField()) #self.universe.protein = self.universe # Set up the subspace: rigid-body translation and rotation for each residue self.subspace = RigidMotionSubspace(self.universe, self.universe.protein.residues())

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MD movie for xyz format
by Jean Didier Pie Marechal 03 Dec '09

03 Dec '09

Dear all, would it be possible to have xyz format accepted for the MD movie tool. Someting identical to the PDB (with both multiple xyz file or unique xyz file containing several structures) would be more than enough. We frequently use this standard and that would be useful for us to have such possbility. All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dilluns, Novembre 23, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 70, Issue 2 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. Rotation about the axis of symmetry (Liam Browne) > 2. Re: Rotation about the axis of symmetry (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 23 Nov 2009 10:06:26 +0000 > From: Liam Browne <liam.browne(a)hotmail.co.uk> > To: <chimera-dev(a)cgl.ucsf.edu> > Subject: [chimera-dev] Rotation about the axis of symmetry > Message-ID: <COL124-W33C2F39CCE1734F40BEB30B69E0(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi all, > > I want to rotate a model by 90 degrees about the axis of symmetry, > but I seem to be having problems setting the axis correctly. > > After two identical models are superimposed I use measure rotation > and get the following: > > Matrix rotation and translation > -0.04092271 -0.36724445 0.92922379 -82.20183653 > -0.91203666 0.39354649 0.11537022 -54.21831923 > -0.40806183 -0.84276490 -0.35104539 11.47082481 > Axis -0.55288898 0.77167664 -0.31437070 > Axis point -56.22800779 0.00000000 25.47389901 > Rotation angle (degrees) 119.94780111 > Shift along axis 0.00338820 > > What should I do to rotate the model at the same axis but by 90 > degrees? > Many thanks, > Liam > > _________________________________________________________________ > View your other email accounts from your Hotmail inbox. Add them now. > http://clk.atdmt.com/UKM/go/186394592/direct/01/ >

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Chimera-dev December 2009