November 2005 - Chimera-dev - RBVI Mailing Lists

add h
by Virginie Lafont 01 May '09

01 May '09

Hi, I am a new user of chimera and I already have a question. I have an protonated aspartic acid in my protein and I was wondering, is it possible to add hydrogen atom to aspartic acid with chimera? Thanks Virginie

4 4

collaboratory tool
by Xavier Deupi 22 Nov '05

22 Nov '05

Hi, In the workshop last week I asked some of you about the collaboratory tool. Well, I'm making some tests and, so far, it has more or less worked between two computers in our lab. Now I want to try 'outside' the university firewall. But during the tests, Chimera has crashed a couple of times when I was joining the session I had just started. I include the error report generated by my computer (a PowerBook G4). I don't think I made anything different the times it has worked than the times the program crashed. Hope the error report makes some sense to you. Thanks, xavi *********************************************** Date/Time: 2005-11-21 13:59:03.443 -0800 OS Version: 10.4.3 (Build 8F46) Report Version: 3 Command: python2.4 Path: /Applications/Chimera.app/Contents/Resources/bin/python2.4 Parent: WindowServer [48] Version: 1.2184 (1.2184) PID: 854 Thread: 0 Exception: EXC_BAD_ACCESS (0x0001) Codes: KERN_INVALID_ADDRESS (0x0001) at 0x7fffdead Thread 0 Crashed: 0 libomniORB4.0.dylib 0x0314b1d8 parse_lsda_header(_Unwind_Context*, unsigned char const*, lsda_header_info*) + 48 (icplusplus.c:27) 1 libomniORB4.0.dylib 0x0314b494 __gxx_personality_v0 + 164 (icplusplus.c:27) 2 _omnipymodule.so 0x030850ac _Unwind_RaiseException_Phase2 + 124 3 _omnipymodule.so 0x03085420 _Unwind_Resume + 104 4 _omnipymodule.so 0x0305c764 omniPy::Py_omniCallDescriptor::userException(cdrStream&, omni::IOP_C*, char const*) + 284 5 libomniORB4.0.dylib 0x031021e4 omniRemoteIdentity::dispatch(omniCallDescriptor&) + 492 (icplusplus.c:27) 6 libomniORB4.0.dylib 0x030e981c omniObjRef::_invoke(omniCallDescriptor&, bool) + 500 (icplusplus.c:27) 7 _omnipymodule.so 0x03052918 omnipy_invoke + 376 8 python2.4 0x0008d3c8 call_function + 948 (ceval.c:3558) 9 python2.4 0x0008ae28 PyEval_EvalFrame + 8852 (ceval.c:2165) 10 python2.4 0x0008bfe0 PyEval_EvalCodeEx + 2156 (ceval.c:2736) 11 python2.4 0x0008d6ac fast_function + 360 (ceval.c:3651) 12 python2.4 0x0008d4a0 call_function + 1164 (ceval.c:3579) 13 python2.4 0x0008ae28 PyEval_EvalFrame + 8852 (ceval.c:2165) 14 python2.4 0x0008d618 fast_function + 212 (ceval.c:3642) 15 python2.4 0x0008d4a0 call_function + 1164 (ceval.c:3579) 16 python2.4 0x0008ae28 PyEval_EvalFrame + 8852 (ceval.c:2165) 17 python2.4 0x0008bfe0 PyEval_EvalCodeEx + 2156 (ceval.c:2736) 18 python2.4 0x0008d6ac fast_function + 360 (ceval.c:3651) 19 python2.4 0x0008d4a0 call_function + 1164 (ceval.c:3579) 20 python2.4 0x0008ae28 PyEval_EvalFrame + 8852 (ceval.c:2165) 21 python2.4 0x0008bfe0 PyEval_EvalCodeEx + 2156 (ceval.c:2736) 22 python2.4 0x0008d6ac fast_function + 360 (ceval.c:3651) 23 python2.4 0x0008d4a0 call_function + 1164 (ceval.c:3579) 24 python2.4 0x0008ae28 PyEval_EvalFrame + 8852 (ceval.c:2165) 25 python2.4 0x0008bfe0 PyEval_EvalCodeEx + 2156 (ceval.c:2736) 26 python2.4 0x000b84f4 function_call + 344 (funcobject.c:548) 27 python2.4 0x0001c2a0 PyObject_Call + 48 (abstract.c:1757) 28 python2.4 0x0008cfd0 PyEval_CallObjectWithKeywords + 256 (ceval.c:3426) 29 python2.4 0x000a48dc builtin_apply + 352 (bltinmodule.c:100) 30 python2.4 0x0008d3c8 call_function + 948 (ceval.c:3558) 31 python2.4 0x0008ae28 PyEval_EvalFrame + 8852 (ceval.c:2165) 32 python2.4 0x0008bfe0 PyEval_EvalCodeEx + 2156 (ceval.c:2736) 33 python2.4 0x000b84f4 function_call + 344 (funcobject.c:548) 34 python2.4 0x0001c2a0 PyObject_Call + 48 (abstract.c:1757) 35 python2.4 0x000869a8 instancemethod_call + 788 (classobject.c:2448) 36 python2.4 0x0001c2a0 PyObject_Call + 48 (abstract.c:1757) 37 python2.4 0x0008cfd0 PyEval_CallObjectWithKeywords + 256 (ceval.c:3426) 38 _tkinter.so 0x0179ccb0 PythonCmd + 368 (_tkinter.c:1999) 39 libtcl8.4.dylib 0x0a00dc94 TclInvokeStringCommand + 148 (icplusplus.c:27) 40 libtcl8.4.dylib 0x0a00ee58 TclEvalObjvInternal + 676 (icplusplus.c:27) 41 libtcl8.4.dylib 0x0a0326ec TclExecuteByteCode + 2536 (icplusplus.c:27) 42 libtcl8.4.dylib 0x0a0319ec Tcl_ExprObj + 1056 (icplusplus.c:27) 43 libtcl8.4.dylib 0x0a010344 Tcl_ExprBooleanObj + 40 (icplusplus.c:27) 44 libtcl8.4.dylib 0x0a016a44 Tcl_IfObjCmd + 80 (icplusplus.c:27) 45 libtcl8.4.dylib 0x0a00ee58 TclEvalObjvInternal + 676 (icplusplus.c:27) 46 libtcl8.4.dylib 0x0a00f6e8 Tcl_EvalEx + 372 (icplusplus.c:27) 47 libtcl8.4.dylib 0x0a00fa2c Tcl_Eval + 32 (icplusplus.c:27) 48 libtcl8.4.dylib 0x0a011008 Tcl_GlobalEval + 36 (icplusplus.c:27) 49 libtk8.4.dylib 0x0b00445c Tk_BindEvent + 1644 (icplusplus.c:27) 50 libtk8.4.dylib 0x0b009f94 TkBindEventProc + 380 (icplusplus.c:27) 51 libtk8.4.dylib 0x0b011ef4 Tk_HandleEvent + 1832 (icplusplus.c:27) 52 libtk8.4.dylib 0x0b0124c4 WindowEventProc + 140 (icplusplus.c:27) 53 libtcl8.4.dylib 0x0a056ff4 Tcl_ServiceEvent + 144 (icplusplus.c:27) 54 libtcl8.4.dylib 0x0a0572dc Tcl_DoOneEvent + 156 (icplusplus.c:27) 55 _tkinter.so 0x0179b1a4 Tkapp_MainLoop + 436 (_tkinter.c:2537) 56 python2.4 0x0008d3c8 call_function + 948 (ceval.c:3558) 57 python2.4 0x0008ae28 PyEval_EvalFrame + 8852 (ceval.c:2165) 58 python2.4 0x0008bfe0 PyEval_EvalCodeEx + 2156 (ceval.c:2736) 59 python2.4 0x0008d6ac fast_function + 360 (ceval.c:3651) 60 python2.4 0x0008d4a0 call_function + 1164 (ceval.c:3579) 61 python2.4 0x0008ae28 PyEval_EvalFrame + 8852 (ceval.c:2165) 62 python2.4 0x0008d618 fast_function + 212 (ceval.c:3642) 63 python2.4 0x0008d4a0 call_function + 1164 (ceval.c:3579) 64 python2.4 0x0008ae28 PyEval_EvalFrame + 8852 (ceval.c:2165) 65 python2.4 0x0008bfe0 PyEval_EvalCodeEx + 2156 (ceval.c:2736) 66 python2.4 0x0008d6ac fast_function + 360 (ceval.c:3651) 67 python2.4 0x0008d4a0 call_function + 1164 (ceval.c:3579) 68 python2.4 0x0008ae28 PyEval_EvalFrame + 8852 (ceval.c:2165) 69 python2.4 0x0008bfe0 PyEval_EvalCodeEx + 2156 (ceval.c:2736) 70 python2.4 0x0008f480 PyEval_EvalCode + 48 (ceval.c:484) 71 python2.4 0x0000cc04 run_node + 76 (pythonrun.c:1266) 72 python2.4 0x0000c360 PyRun_SimpleFileExFlags + 604 (pythonrun.c:863) 73 python2.4 0x000067a0 Py_Main + 2708 (main.c:484) 74 python2.4 0x00002150 _start + 380 (crt.c:267) 75 python2.4 0x00001fd0 start + 48 Thread 1: 0 libSystem.B.dylib 0x90053f68 semaphore_timedwait_signal_trap + 8 1 libSystem.B.dylib 0x90053dc8 pthread_cond_timedwait + 672 2 libomnithread.3.dylib 0x0325432c omni_condition::timedwait(unsigned long, unsigned long) + 56 (icplusplus.c:27) 3 _omnipymodule.so 0x0307cf38 omnipyThreadScavenger::run_undetached(void*) + 228 4 libomnithread.3.dylib 0x03254958 omni_thread_wrapper + 208 (icplusplus.c:27) 5 libSystem.B.dylib 0x9002b200 _pthread_body + 96 Thread 2: 0 libSystem.B.dylib 0x9001f20c select + 12 1 libomniORB4.0.dylib 0x03126c50 omni::SocketCollection::Select() + 352 (icplusplus.c:27) 2 libomniORB4.0.dylib 0x031448a8 omni::tcpEndpoint::AcceptAndMonitor(void (*)(void*, omni::giopConnection*), void*) + 124 (icplusplus.c:27) 3 libomniORB4.0.dylib 0x03115788 omni::giopRendezvouser::execute() + 196 (icplusplus.c:27) 4 libomniORB4.0.dylib 0x03186b64 omniAsyncWorker::real_run() + 528 (icplusplus.c:27) 5 libomniORB4.0.dylib 0x03186940 omniAsyncWorker::run(void*) + 68 (icplusplus.c:27) 6 libomnithread.3.dylib 0x03254938 omni_thread_wrapper + 176 (icplusplus.c:27) 7 libSystem.B.dylib 0x9002b200 _pthread_body + 96 Thread 3: 0 libSystem.B.dylib 0x90053f68 semaphore_timedwait_signal_trap + 8 1 libSystem.B.dylib 0x90053dc8 pthread_cond_timedwait + 672 2 libomnithread.3.dylib 0x0325432c omni_condition::timedwait(unsigned long, unsigned long) + 56 (icplusplus.c:27) 3 libomniORB4.0.dylib 0x0310fa34 omni::Scavenger::execute() + 180 (icplusplus.c:27) 4 libomniORB4.0.dylib 0x03186b64 omniAsyncWorker::real_run() + 528 (icplusplus.c:27) 5 libomniORB4.0.dylib 0x03186940 omniAsyncWorker::run(void*) + 68 (icplusplus.c:27) 6 libomnithread.3.dylib 0x03254938 omni_thread_wrapper + 176 (icplusplus.c:27) 7 libSystem.B.dylib 0x9002b200 _pthread_body + 96 Thread 4: 0 libSystem.B.dylib 0x90023420 recvfrom + 12 1 libomniORB4.0.dylib 0x03143470 omni::tcpConnection::Recv(void*, unsigned long, unsigned long, unsigned long) + 304 (icplusplus.c:27) 2 libomniORB4.0.dylib 0x031116b4 omni::giopStream::inputMessage() + 336 (icplusplus.c:27) 3 libomniORB4.0.dylib 0x03120150 omni::giopImpl12::inputNewServerMessage(omni::giopStream*) + 72 (icplusplus.c:27) 4 libomniORB4.0.dylib 0x03120704 omni::giopImpl12::inputMessageBegin(omni::giopStream*, void (*)(omni::giopStream*)) + 208 (icplusplus.c:27) 5 libomniORB4.0.dylib 0x03116f04 omni::GIOP_S::dispatcher() + 100 (icplusplus.c:27) 6 libomniORB4.0.dylib 0x03115648 omni::giopWorker::real_execute() + 1472 (icplusplus.c:27) 7 libomniORB4.0.dylib 0x03115074 omni::giopWorker::execute() + 68 (icplusplus.c:27) 8 libomniORB4.0.dylib 0x03186b64 omniAsyncWorker::real_run() + 528 (icplusplus.c:27) 9 libomniORB4.0.dylib 0x03186940 omniAsyncWorker::run(void*) + 68 (icplusplus.c:27) 10 libomnithread.3.dylib 0x03254938 omni_thread_wrapper + 176 (icplusplus.c:27) 11 libSystem.B.dylib 0x9002b200 _pthread_body + 96 Thread 0 crashed with PPC Thread State 64: srr0: 0x000000000314b1d8 srr1: 0x000000000200f030 vrsave: 0x0000000000000000 cr: 0x84002242 xer: 0x0000000020000004 lr: 0x000000000314b1cc ctr: 0x00000000913aff58 r0: 0x000000000314b1cc r1: 0x00000000bfffba00 r2: 0x00000000a0001fa8 r3: 0x000000007fffdead r4: 0x000000007fffdead r5: 0x00000000bfffbab0 r6: 0x00000000432b2b00 r7: 0x0000000000697e80 r8: 0x00000000bfffc150 r9: 0x0000000000000008 r10: 0x00000000ffeaf704 r11: 0x000000000319acb0 r12: 0x00000000913aff58 r13: 0x00000000000f8ba0 r14: 0x0000000003291570 r15: 0x0000000000000000 r16: 0x0000000000000000 r17: 0x0000000000000000 r18: 0x000000007fffdead r19: 0x0000000000000000 r20: 0x0000000000000002 r21: 0x0000000000600160 r22: 0x00000000032e5970 r23: 0x0000000000000001 r24: 0x00000000bfffc150 r25: 0x0000000000697e50 r26: 0x00000000474e5543 r27: 0x00000000bfffbab0 r28: 0x0000000000697e80 r29: 0x00000000bfffc150 r30: 0x000000007fffdead r31: 0x0000000003085040 Binary Images Description: 0x1000 - 0xedfff python2.4 /Applications/Chimera.app/Contents/Resources/bin/python2.4 0x3d6000 - 0x3d6fff _chimera.so /Applications/Chimera.app/Contents/Resources/lib/_chimera.so 0x3d9000 - 0x3dbfff libtr.dylib /Applications/Chimera.app/Contents/Resources/lib/libtr.dylib 0x3e6000 - 0x3e7fff math.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/math.so 0x545000 - 0x576fff libwrappy2.dylib /Applications/Chimera.app/Contents/Resources/lib/libwrappy2.dylib 0x5a5000 - 0x5acfff libtogl.dylib /Applications/Chimera.app/Contents/Resources/lib/libtogl.dylib 0x5ce000 - 0x5d1fff strop.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/strop.so 0x5e3000 - 0x5e4fff MacOS.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/MacOS.so 0x705000 - 0x7a6fff libotf.dylib /Applications/Chimera.app/Contents/Resources/lib/libotf.dylib 0x1008000 - 0x1207fff _chimera.dylib /Applications/Chimera.app/Contents/Resources/lib/_chimera.dylib 0x138e000 - 0x13a1fff libftgl.dylib /Applications/Chimera.app/Contents/Resources/lib/libftgl.dylib 0x1466000 - 0x14a7fff libfreetype.6.dylib /Applications/Chimera.app/Contents/Resources/lib/libfreetype.6.dylib 0x1604000 - 0x1652fff libz.dylib /Applications/Chimera.app/Contents/Resources/lib/libz.dylib 0x1694000 - 0x16fffff _vrml.so /Applications/Chimera.app/Contents/Resources/lib/_vrml.so 0x1796000 - 0x179efff _tkinter.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/_tkinter.so 0x2048000 - 0x204afff operator.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/operator.so 0x2059000 - 0x2059fff _weakref.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/_weakref.so 0x2065000 - 0x2067fff cStringIO.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/cStringIO.so 0x2116000 - 0x2118fff binascii.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/binascii.so 0x2127000 - 0x2128fff _random.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/_random.so 0x2135000 - 0x2136fff fcntl.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/fcntl.so 0x2144000 - 0x2188fff _imaging.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/site-packages/PIL/_imaging.so 0x2276000 - 0x227bfff array.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/array.so 0x2290000 - 0x2290fff _imagingtk.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/site-packages/PIL/_imagingtk.so 0x22c1000 - 0x22c3fff _ssl.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/_ssl.so 0x235a000 - 0x2361fff _socket.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/_socket.so 0x237c000 - 0x237efff time.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/time.so 0x2458000 - 0x248bfff libtix8.2.dylib /Applications/Chimera.app/Contents/Resources/lib/libtix8.2.dylib 0x265c000 - 0x2675fff GLDriver /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLDriver.bundle/GLDriver 0x267b000 - 0x2696fff GLRendererFloat /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat 0x2805000 - 0x2914fff GLEngine /System/Library/Frameworks/OpenGL.framework/Resources/GLEngine.bundle/GLEngine 0x2943000 - 0x2b9afff com.apple.ATIRadeon8500GLDriver 1.4.16 (4.1.6) /System/Library/Extensions/ATIRadeon8500GLDriver.bundle/Contents/MacOS/ATIRadeon8500GLDriver 0x2c45000 - 0x2c49fff _AE.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/_AE.so 0x2c6b000 - 0x2c6dfff _Evt.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/_Evt.so 0x2c8b000 - 0x2c8efff struct.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/struct.so 0x2cac000 - 0x2cb4fff _File.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/_File.so 0x2d69000 - 0x2d98fff _collaboratory.so /Applications/Chimera.app/Contents/Resources/lib/_collaboratory.so 0x2f5e000 - 0x2f63fff _Res.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/_Res.so 0x3030000 - 0x3031fff termios.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/termios.so 0x303e000 - 0x3040fff collections.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/collections.so 0x3050000 - 0x3097fff _omnipymodule.so /Applications/Chimera.app/Contents/Resources/lib/_omnipymodule.so 0x30c0000 - 0x3197fff libomniORB4.0.dylib /Applications/Chimera.app/Contents/Resources/lib/libomniORB4.0.dylib 0x3253000 - 0x325dfff libomnithread.3.dylib /Applications/Chimera.app/Contents/Resources/lib/libomnithread.3.dylib 0x32ee000 - 0x32fdfff cPickle.so /Applications/Chimera.app/Contents/Resources/lib/python2.4/lib-dynload/cPickle.so 0xa000000 - 0xa089fff libtcl8.4.dylib /Applications/Chimera.app/Contents/Resources/lib/libtcl8.4.dylib 0xb000000 - 0xb0b1fff libtk8.4.dylib /Applications/Chimera.app/Contents/Resources/lib/libtk8.4.dylib 0x8fe00000 - 0x8fe54fff dyld 44.2 /usr/lib/dyld 0x90000000 - 0x901b3fff libSystem.B.dylib /usr/lib/libSystem.B.dylib 0x9020b000 - 0x9020ffff libmathCommon.A.dylib /usr/lib/system/libmathCommon.A.dylib 0x90211000 - 0x90264fff com.apple.CoreText 1.0.1 (???) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreText.framework/Versions/A/CoreText 0x90291000 - 0x90342fff ATS /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS 0x90371000 - 0x906aefff com.apple.CoreGraphics 1.256.27 (???) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics 0x9073a000 - 0x90813fff com.apple.CoreFoundation 6.4.4 (368.18) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 0x9085c000 - 0x9085cfff com.apple.CoreServices 10.4 (???) /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices 0x9085e000 - 0x90960fff libicucore.A.dylib /usr/lib/libicucore.A.dylib 0x909ba000 - 0x90a3efff libobjc.A.dylib /usr/lib/libobjc.A.dylib 0x90a68000 - 0x90ad6fff com.apple.framework.IOKit 1.4 (???) /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit 0x90aed000 - 0x90afffff libauto.dylib /usr/lib/libauto.dylib 0x90b06000 - 0x90dddfff com.apple.CoreServices.CarbonCore 671.2 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore 0x90e43000 - 0x90ec3fff com.apple.CoreServices.OSServices 4.1 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices 0x90f0d000 - 0x90f4efff com.apple.CFNetwork 10.4.3 (129.2) /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/Versions/A/CFNetwork 0x90f63000 - 0x90f7bfff com.apple.WebServices 1.1.2 (1.1.0) /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/WebServicesCore.framework/Versions/A/WebServicesCore 0x90f8b000 - 0x9100cfff com.apple.SearchKit 1.0.4 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/SearchKit 0x91052000 - 0x9107bfff com.apple.Metadata 10.4.3 (121.20.2) /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata 0x9108c000 - 0x9109afff libz.1.dylib /usr/lib/libz.1.dylib 0x9109d000 - 0x9125ffff com.apple.security 4.2 (24844) /System/Library/Frameworks/Security.framework/Versions/A/Security 0x91362000 - 0x9136bfff com.apple.DiskArbitration 2.1 /System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration 0x91372000 - 0x91399fff com.apple.SystemConfiguration 1.8.1 /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration 0x913ac000 - 0x913b4fff libgcc_s.1.dylib /usr/lib/libgcc_s.1.dylib 0x913b9000 - 0x913d9fff libmx.A.dylib /usr/lib/libmx.A.dylib 0x913df000 - 0x913e7fff libbsm.dylib /usr/lib/libbsm.dylib 0x913eb000 - 0x91469fff com.apple.audio.CoreAudio 3.0.1 /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio 0x914a7000 - 0x914a7fff com.apple.ApplicationServices 10.4 (???) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices 0x914a9000 - 0x914e1fff com.apple.AE 1.5 (297) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE 0x914fc000 - 0x915c9fff com.apple.ColorSync 4.4.3 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync 0x9161e000 - 0x916b1fff com.apple.print.framework.PrintCore 4.3 (172.3) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore 0x916f8000 - 0x917b5fff com.apple.QD 3.8.18 (???) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD 0x917f3000 - 0x91851fff com.apple.HIServices 1.5.1 (???) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices 0x9187f000 - 0x918a3fff com.apple.LangAnalysis 1.6.1 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis 0x918b7000 - 0x918dcfff com.apple.FindByContent 1.5 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/FindByContent.framework/Versions/A/FindByContent 0x918ef000 - 0x91931fff com.apple.LaunchServices 10.4.5 (168) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices 0x9194d000 - 0x91961fff com.apple.speech.synthesis.framework 3.3 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis 0x9196f000 - 0x919a8fff com.apple.ImageIO.framework 1.4.3 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO 0x919bd000 - 0x91a83fff libcrypto.0.9.7.dylib /usr/lib/libcrypto.0.9.7.dylib 0x91ad0000 - 0x91ae5fff libcups.2.dylib /usr/lib/libcups.2.dylib 0x91aea000 - 0x91b06fff libJPEG.dylib /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib 0x91b0b000 - 0x91b7afff libJP2.dylib /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib 0x91b91000 - 0x91b95fff libGIF.dylib /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib 0x91b97000 - 0x91bc8fff libRaw.dylib /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libRaw.dylib 0x91bcc000 - 0x91c0ffff libTIFF.dylib /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib 0x91c16000 - 0x91c2ffff libPng.dylib /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib 0x91c34000 - 0x91c37fff libRadiance.dylib /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib 0x91c39000 - 0x91c39fff com.apple.Accelerate 1.1.1 (Accelerate 1.1.1) /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate 0x91c3b000 - 0x91d25fff com.apple.vImage 2.0 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage 0x91d2d000 - 0x91d4cfff com.apple.Accelerate.vecLib 3.1.1 (vecLib 3.1.1) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib 0x91db8000 - 0x91e1dfff libvMisc.dylib /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib 0x91e27000 - 0x91eb9fff libvDSP.dylib /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib 0x91ed3000 - 0x92463fff libBLAS.dylib /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 0x924ab000 - 0x927bbfff libLAPACK.dylib /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib 0x927e8000 - 0x92874fff com.apple.DesktopServices 1.3.1 /System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv 0x928b6000 - 0x92ae0fff com.apple.Foundation 6.4.2 (567.21) /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation 0x92bfe000 - 0x92cdcfff libxml2.2.dylib /usr/lib/libxml2.2.dylib 0x92cfc000 - 0x92deafff libiconv.2.dylib /usr/lib/libiconv.2.dylib 0x92dfc000 - 0x92e1afff libGL.dylib /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib 0x92e25000 - 0x92e7ffff libGLU.dylib /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib 0x92e9d000 - 0x92e9dfff com.apple.Carbon 10.4 (???) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon 0x92e9f000 - 0x92eb3fff com.apple.ImageCapture 3.0 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture 0x92ecb000 - 0x92edbfff com.apple.speech.recognition.framework 3.4 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/Versions/A/SpeechRecognition 0x92ee7000 - 0x92efcfff com.apple.securityhi 2.0 (203) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI 0x92f0e000 - 0x92f95fff com.apple.ink.framework 101.2 (69) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink 0x92fa9000 - 0x92fb4fff com.apple.help 1.0.3 (32) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Help.framework/Versions/A/Help 0x92fbe000 - 0x92febfff com.apple.openscripting 1.2.3 (???) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting 0x93005000 - 0x93015fff com.apple.print.framework.Print 5.0 (190.1) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print 0x93021000 - 0x93087fff com.apple.htmlrendering 1.1.2 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HTMLRendering.framework/Versions/A/HTMLRendering 0x930b8000 - 0x9310afff com.apple.NavigationServices 3.4.2 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/NavigationServices.framework/Versions/A/NavigationServices 0x93136000 - 0x93153fff com.apple.audio.SoundManager 3.9 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CarbonSound.framework/Versions/A/CarbonSound 0x93165000 - 0x93172fff com.apple.CommonPanels 1.2.2 (73) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/A/CommonPanels 0x9317b000 - 0x9348dfff com.apple.HIToolbox 1.4.4 (???) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox 0x935d9000 - 0x935e5fff com.apple.opengl 1.4.6 /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL 0x94407000 - 0x94457fff libGLImage.dylib /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib 0x94ce0000 - 0x94d0efff libssl.0.9.7.dylib /usr/lib/libssl.0.9.7.dylib 0x97afa000 - 0x97bbbfff libGLProgrammability.dylib /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib 0x97be6000 - 0x97be7fff libGLSystem.dylib /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLSystem.dylib 0x9b0a0000 - 0x9b0affff libICE.6.dylib /usr/X11R6/lib/libICE.6.dylib 0x9b0b5000 - 0x9b0bafff libSM.6.dylib /usr/X11R6/lib/libSM.6.dylib 0x9b1cb000 - 0x9b1d9fff libXplugin.1.dylib /usr/lib/libXplugin.1.dylib 0x9c1be000 - 0x9c1c9fff libXext.6.dylib /usr/X11R6/lib/libXext.6.dylib 0x9c1ce000 - 0x9c296fff libX11.6.2.dylib /usr/X11R6/lib/libX11.6.2.dylib 0x9c2bd000 - 0x9c337fff libGL.1.2.dylib /usr/X11R6/lib/libGL.1.2.dylib 0x9c366000 - 0x9c3c8fff libGLU.1.3.dylib /usr/X11R6/lib/libGLU.1.3.dylib 0x9c55e000 - 0x9c5a0fff libXt.6.0.dylib /usr/X11R6/lib/libXt.6.0.dylib 0x9c5ef000 - 0x9c5fffff libXmu.6.2.dylib /usr/X11R6/lib/libXmu.6.2.dylib Model: PowerBook3,5, BootROM 4.5.3f2, 1 processors, PowerPC G4 (3.2), 1 GHz, 1 GB Graphics: ATY,RV250M9, ATY,RV250M9, AGP, 64 MB Memory Module: SODIMM0/J16TOP, 512 MB, SDRAM, PC133U-333 Memory Module: SODIMM1/J16BOTTOM, 512 MB, SDRAM, PC133U-333 AirPort: AirPort, 9.52 Modem: MicroDash, UCJ, V.92, 1.0F, APPLE VERSION 2.6.6 Network Service: Built-in Ethernet, Ethernet, en0 Network Service: AirPort, AirPort, en1 PCI Card: TXN,PCI1410-02, cardbus, PC Card Parallel ATA Device: HTE726060M9AT00, 55.89 GB Parallel ATA Device: MATSHITADVD-R UJ-815, USB Device: USB2.0 Hub, , Up to 12 Mb/sec, 500 mA USB Device: Hub in Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec, 500 mA USB Device: Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec, 250 mA USB Device: USB-PS/2 Optical Mouse, Logitech, Up to 1.5 Mb/sec, 500 mA USB Device: Creative Zen Micro, Creative Technology Ltd, Up to 12 Mb/sec, 500 mA FireWire Device: unknown_device, unknown_value, Up to 400 Mb/sec -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genetic Medicine (B161) 279 Campus Drive, Stanford University School of Medicine Stanford, CA 94305 (USA) E-mail: Xavier.Deupi(a)stanford.edu Phone: +1 (650) 725-6497 Fax : +1 (650) 725-8021

2 1

Reference Manual
by Reiner Villavicencio 17 Nov '05

17 Nov '05

Dear Chimera Staff, I was wondering where can I get an offline reference manual (*.pdf) for Chimera if there is any? I noticed that the documentation site only has user guides available for online viewing. Or will you be putting together something like that soon? Thank you and good day Reiner Villavicencio BS Biochemistry Dept. of Physical Sciences and Mathematics College of Arts and Sciences University of the Philippines, Manila "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

1 0

Re: [chimera-dev] [Chimera-users] Rotation callback
by Eric Pettersen 11 Nov '05

11 Nov '05

Hi Charlie, The answer is: sort of. You can't get a callback for when a specific model moves, but you can get callbacks for when any models move and from there it's pretty easy to deduce if models you are interested in moved. There are two possible triggers you could use. The one most typically used is chimera.MOTION_STOP (mentioned in the Trigger Notifications programming example), which fires one second after models have stopped moving (the motion can be due to user interaction or programmatic repositioning). On the assumption that what you want to do in response to the trigger is somewhat heavyweight, this is the trigger you would want to use. The other trigger is 'OpenState', which will fire many times as a motion occurs. If you use this trigger, you could check to see if the trigger data's 'modified' attribute contains the OpenState instance of the model(s) you care about and whether the trigger data's 'reasons' attribute contains the string "transformation change". There is an OpenState instance for each model ID/subID pair. So some models share a single OpenState instance (e.g. a structure model and corresponding surface model). Models have an 'openState' attribute, and OpenState instances have an 'xform' attribute containing the transformation matrix. If you use the MOTION_STOP trigger, you would compare the transforms of the models you care about with previous ones that you'd saved to determine if the models had moved. UndoMove is an example of an extension that uses MOTION_STOP. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu On Nov 10, 2005, at 12:06 PM, Charlie Moad wrote: > Is it possible to register a python callback for when a protein is > rotated and get the rotation information? > > Thanks, > Charlie > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

Re: [chimera-dev] [Chimera-users] chimera and STRAP ?
by Greg Couch 01 Nov '05

01 Nov '05

On Sun, 30 Oct 2005, Dr. Christoph Gille wrote: > I contact you because users of the program STRAP for protein > structures and sequences asked whether Chimera could be used within > STRAP for visualization. > > Currently Jmol and Pymol are used for visualiziation. For example the > results of 3D superpositions and the location of mutations can be > viewed. But some users apparently prefere Chimera. > > My question is whether Chimera could be linked to STRAP as well. The > most important point is, what mode of interprocess commmunication > exists in Chimera. > > For example Pymol and STRAP are linked via the stdin/stdout streams. > STRAP can send commands to Pymol and is notified when atoms are picked. > > STRAP uses the scripting language of Pymol to load proteins, create > selections and rotate proteins. > Could all this be done with Chimera in a similar way ? (Replies should be sent to chimera-dev(a)cgl.ucsf.edu) Sending commands and data to chimera can be done with the --send command line argument that was added for web browser support (it's not enabled by default except on Mac OS X, use Tools/Preferences Web Access to "Accept web data"). For bidirectional communication, you'll need to add some Python code -- python supports the same IPC that the underlying C library does, but the IPC should be integrated into the chimera event loop -- look at the socket code from CHIMERA/share/DBPuppet/tcl_sockets.py to see an example of integrating Internet sockets. Internet sockets are the general solution because standard input and output can only be used by one other appliction, but there are security issues. Chimera uses a shared key (read from the filesystem) security protocol to prevent hijacking of the web browser connection. I'd also recommend creating a chimera extension with all of the STRAP related code in it. For examples on how to do that, see the Chimera Programmer's Guide examples, <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html>. The examples also show how to use chimera selections pragrammatically. So the answer is yes, chimera could be linked to STRAP. I hope this answer gives you some ideas on how to proceed. I would be delighted to work with you to get the programs working together. Greg Couch UCSF Computer Graphics Lab gregc(a)cgl.ucsf.edu

1 0

Chimera-dev November 2005