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

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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 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/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

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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

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Re: [chimera-dev] [Chimera-users] Rotation callback
by Eric Pettersen 12 Nov '05

12 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

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Re: [chimera-dev] [Chimera-users] chimera and STRAP ?
by Greg Couch 02 Nov '05

02 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

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