- Chimera-dev - RBVI Mailing Lists

adding an atom at the centroid of a blob
by Jean Didier Pie Marechal 14 Jan '10

14 Jan '10

Hi everyone, I have obtained cavities for a given atom selection using surfnet and I want to put an atom at the centroid of the main blob. I know how to do this for a selected set of atom but I am struggling with the surfaces. At this point, I splitted it (accelator Sc) and then I can select the blob I am interested in. But how could I create a particular object for this blob? From there, how could I add an atom (i.e. helium) and the centroid of the blob? Thanks for any help, 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: Dimarts, Desembre 15, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 71, Issue 4 > 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. Re: [Chimera-users] Programmer's Guide feedback.... > (Eric Pettersen) > 2. Re: [Chimera-users] Programmer's Guide feedback.... (Tom > Goddard) 3. Re: [Chimera-users] Programmer's Guide feedback.... > (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 15 Dec 2009 10:55:42 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] [Chimera-users] Programmer's Guide > feedback.... > Message-ID: <61EC3E93-8EE5-48E0-AB71-4705D5162EE4(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > 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 > > >

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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 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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 + 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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 ??? 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(???) /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 ??? 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(???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/_sort.so 0x1f5a000 - 0x1f67fff +cPickle.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/cPickle.so 0x1fc6000 - 0x1fc7fe3 +time.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/time.so 0x1fd1000 - 0x1fd3ffb +_compiled_base.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/_compiled_base.so 0x1fdd000 - 0x1fe0fff +itertools.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/itertools.so 0x1ff0000 - 0x1ff0ffd +gestalt.so ??? 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(???) /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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(???) <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 ??? 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(???) <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 ??? 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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 ??? (???) <769EF4B2-C1AD-73D5-AAAD-1564DAEA77AF> /usr/lib/libxslt.1.dylib 0x98b35000 - 0x98b53ff7 com.apple.CoreVideo 1.6.0 (43.1) <1FB01BE0-B013-AE86-A063-481BB547D2F5> /System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo 0x98d0d000 - 0x98de7ff3 com.apple.DesktopServices 1.5.3 (1.5.3) <DA02AC94-7B0C-BD75-2305-C46A307A5FB0> /System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv 0x98de8000 - 0x98e0cff7 libJPEG.dylib ??? (???) <649E1974-A527-AC0B-B3F4-B4DC30484070> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib 0x98e0d000 - 0x98e25ff7 com.apple.CFOpenDirectory 10.6 (10.6) <1537FB4F-C112-5D12-1E5D-3B1002A4038F> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory 0x98e26000 - 0x98ea8ffb SecurityFoundation ??? (???) <29C27E0E-B2B3-BF6B-B1F8-5783B8B01535> /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/SecurityFoundation 0x98eea000 - 0x98fc5ff7 com.apple.DiscRecording 5.0.3 (5030.4.2) <CC86EBA6-5E48-32C0-77AE-81479DFF6D4A> /System/Library/Frameworks/DiscRecording.framework/Versions/A/DiscRecording 0x9900a000 - 0x99050ff7 libauto.dylib ??? (???) <85670A64-3B67-8162-D441-D8E0BE15CA94> /usr/lib/libauto.dylib 0x9908e000 - 0x990d2ff3 com.apple.coreui 2 (113) <D0FA9B36-3708-D5BF-0CC3-6CC1909BC8E6> /System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI 0x9920c000 - 0x992c5fe7 libsqlite3.dylib ??? (???) <16CEF8E8-8C9A-94CD-EF5D-05477844C005> /usr/lib/libsqlite3.dylib 0x992c6000 - 0x992c7ff7 com.apple.TrustEvaluationAgent 1.1 (1) <6C04C4C5-667E-2EBE-EB96-5B67BD4B2185> /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent 0x992d0000 - 0x992d4ff7 IOSurface ??? (???) <C11D3FF3-EB51-A07D-EF24-9C2004115724> /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface 0x992d5000 - 0x99344ff7 libvMisc.dylib ??? (???) <59243A8C-2B98-3E71-8032-884D4853E79F> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib 0x99417000 - 0x994c5ff3 com.apple.ink.framework 1.3.1 (105) <CA3FBDC3-4BBA-7BD9-0777-A7B0751292CD> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink 0xba900000 - 0xba916ff7 libJapaneseConverter.dylib ??? (???) <4FB5CEEB-8D3E-8C57-1718-81D7CAFBFE69> /System/Library/CoreServices/Encodings/libJapaneseConverter.dylib 0xbab00000 - 0xbab21fe7 libKoreanConverter.dylib ??? (???) <A23F9980-5CC8-A44D-6FD6-DBFCBFF4FF28> /System/Library/CoreServices/Encodings/libKoreanConverter.dylib 0xeab00000 - 0xeab10fe7 libConverter.dylib ??? (???) <BFC392EC-73AE-D085-9D5A-63399463FD6D> /System/Library/Printers/Libraries/libConverter.dylib 0xffff0000 - 0xffff1fff libSystem.B.dylib ??? (???) <D45B91B2-2B4C-AAC0-8096-1FC48B7E9672> /usr/lib/libSystem.B.dylib Model: MacBookPro2,2, BootROM MBP22.00A5.B07, 2 processors, Intel Core 2 Duo, 2.33 GHz, 3 GB, SMC 1.12f5 Graphics: ATI Radeon X1600, ATY,RadeonX1600, PCIe, 256 MB Memory Module: global_name AirPort: spairport_wireless_card_type_airport_extreme (0x168C, 0x87), Atheros 5416: 2.0.19.4 Bluetooth: Version 2.2.4f3, 2 service, 1 devices, 1 incoming serial ports Network Service: AirPort, AirPort, en1 Network Service: Rice, IPSec, utun0 Serial ATA Device: Hitachi HTS541616J9SA00, 149.05 GB Parallel ATA Device: HL-DT-ST DVDRW GWA4080MA USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8501, 0xfd400000 USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.), 0x021a, 0x1d200000 USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8205, 0x7d100000 USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8240, 0x5d200000

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implementing MMTK normal calculations in chimera
by Victor Muñoz 08 Dec '09

08 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/ >

2 1

Rotation about the axis of symmetry
by Liam Browne 23 Nov '09

23 Nov '09

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/

2 1

writing atom information using the mol2 atom order.
by Jean Didier Pie Marechal 03 Nov '09

03 Nov '09

Dear all, I have a mol2 file and I would like to generate an input for an external program using chimera. For a great ease in practicability, I would like the mol2 order to be kept. I used the following artefact to get to what I want: def input(molecule): ##for compatibility with mol2 atom ordering I use the doble loop as follow ##makes the writing substantially slower, but yet the compatibility with mol2 format seems absolute. for i in range(len(molecule.atoms)): for atoms in molecule.atoms: if atoms.serialNumber == i: text=str(atoms.element)+"-"+str(atoms.gaffType)+"-"+str(atoms.charge)+" "+str(atoms.flex)+" "+str(atoms.coord()) +"\n" filename.write(text) i=i+1 I think I could order directly the writing in function of the serialNumber (which is preserved regarding the mol2) file. But how could I do this? 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

2 1

writing atom information using the mol2 atom order.
by Jean Didier Pie Marechal 03 Nov '09

03 Nov '09

Dear all, I have a mol2 file and I would like to generate an input for an external program using chimera. For a great ease in practicability, I would like the mol2 order to be kept. I used the following artefact to get to what I want: def input(molecule): ##for compatibility with mol2 atom ordering I use the doble loop as follow ##makes the writing substantially slower, but yet the compatibility with mol2 format seems absolute. for i in range(len(molecule.atoms)): for atoms in molecule.atoms: if atoms.serialNumber == i: text=str(atoms.element)+"-"+str(atoms.gaffType)+"-"+str(atoms.charge)+" "+str(atoms.flex)+" "+str(atoms.coord()) +"\n" filename.write(text) i=i+1 I think I could order directly the writing in function of the serialNumber (which is preserved regarding the mol2) file. But how could I do this? 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, Octubre 26, 2009 8:00 pm Assumpte: Chimera-dev Digest, Vol 69, Issue 1 > 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. thank you so much (Corey Fugate) > 2. Re: thank you so much (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 23 Oct 2009 16:57:11 -1000 > From: Corey Fugate <fugate(a)hawaii.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: [chimera-dev] thank you so much > Message-ID: <D445EAAC-78D8-4394-85E0-997DBED43CD8(a)hawaii.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > I started using Chimera a few weeks ago. It is wonderful, I love it. > > > ------------------------------ > > Message: 2 > Date: Mon, 26 Oct 2009 11:03:55 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: Corey Fugate <fugate(a)hawaii.edu> > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] thank you so much > Message-ID: <26F83250-86D7-4E19-8B17-304418C8169D(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > So glad you like it. And always struggling to make it better. > Thanks! :-) > > --Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Oct 23, 2009, at 7:57 PM, Corey Fugate wrote: > > > I started using Chimera a few weeks ago. It is wonderful, I > love it. > > _______________________________________________ > > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > >

1 0

thank you so much
by Corey Fugate 26 Oct '09

26 Oct '09

I started using Chimera a few weeks ago. It is wonderful, I love it.

2 1

select opt
by Victor MuÃ±oz 23 Sep '09

23 Sep '09

Dear Mr/Miss: I'd like to know if there's a way to select the select mode "append" using the command line instead of the visual interface. Thanks for your help. Your sincerelly, Victor Muñoz

3 2