October 2006 - 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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_surface module
by Karin Gross 12 Oct '06

12 Oct '06

Hi, I've tried to display several three-dimensional geometric surfaces in Chimera. I've described the surfaces as sets of quadrilaterals. In Chimera-1.2199 it works, but in Chimera-1.2255 it gives me this error message: ***error: Triangles array second dimension must = 3, got size 4****. Is desribing surfaces as sets of quadrilaterals not supported anymore? Thanks -Karin --------------------------------------------------------------------- This message was sent using https://webmail.biochem.mpg.de If you encounter any problems please report to rz-linux(a)biochem.mpg.de

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chimera import
by Javier Díez 03 Oct '06

03 Oct '06

Hy, I've just started working on a Chimera extension. I've tried to import chimera after setting up the CHIMERA os variable, but it gives me this erro message: ***from _chimera import * ImportError: No module named _chimera *Some help? Thank you. Javi * *

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Re: [chimera-dev] Crash running Chimera benchmark
by Thomas Goddard 02 Oct '06

02 Oct '06

Hi Dave, I wrote the Chimera surface / mesh / volume benchmark tests to try to give a realistic estimate of overall system performance, stressing GPU, CPU speed and memory size. When you have a fast GPU, performance on large data sets can be limited by available memory. Unfortunately memory allocations are done in hundreds of places and often not checked for failure so high memory use can lead to crashes. Sometimes individually running benchmarks (surface , mesh, solid, ...) allows them to work in cases where running them all with the All button causes a crash because of differing memory utilization. Tom

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Crash running Chimera benchmark
by David E. Konerding 02 Oct '06

02 Oct '06

Hi, I get a seg fault when running the Chimera benchmark on my new machine (too bad-- it was coming up with some decent numbers). Here is the backtrace: #0 0xf7dc908d in memmove () from /lib/libc.so.6 #1 0xf582b806 in do_sliced_copy (dest=0xeeb53000 <Address 0xeeb53000 out of bounds>, dest_strides=0x8692b44, dest_dimensions=0x8208d94, dest_nd=-431252312, src=0x8699358 "", src_strides=0x0, src_dimensions=0x0, src_nd=0, elsize=4, copies=4) at Src/arrayobject.c:70 #2 0xf582b894 in do_sliced_copy (dest=0xeeb52ff8 "", dest_strides=0x8692b40, dest_dimensions=0x8208d90, dest_nd=-431252312, src=0x8699358 "", src_strides=0x0, src_dimensions=0x0, src_nd=0, elsize=4, copies=4) at Src/arrayobject.c:78 #3 0xf582b894 in do_sliced_copy (dest=0xeeb50888 "", dest_strides=0x8692b3c, dest_dimensions=0x8208d8c, dest_nd=-431252312, src=0x8699358 "", src_strides=0x0, src_dimensions=0x0, src_nd=0, elsize=4, copies=4) at Src/arrayobject.c:78 #4 0xf582b894 in do_sliced_copy (dest=0xeeac0408 "", dest_strides=0x8692b38, dest_dimensions=0x8208d88, dest_nd=-431252312, src=0x8699358 "", src_strides=0x0, src_dimensions=0x0, src_nd=0, elsize=4, copies=4) at Src/arrayobject.c:78 #5 0xf582bf3f in PyArray_CopyArray (dest=0xf58b87a0, src=0xbaea3008) at Src/arrayobject.c:278 #6 0xf582c02e in PyArray_CopyObject (dest=0xf58b87a0, src_object=0xf58b89a8) at Src/arrayobject.c:315 #7 0xf5833416 in array_ass_sub (self=0xf58b8778, index=0xf58b87a0, op=0x8156f18) at Src/arrayobject.c:1005 #8 0x08058e71 in PyObject_SetItem (o=0xf58b8778, key=0x812dd00, value=0x8156f18) at Objects/abstract.c:123 #9 0x080aeb57 in PyEval_EvalFrame (f=0x84bfdcc) at Python/ceval.c:1474 #10 0x080b098e in PyEval_EvalCodeEx (co=0xf5899ca0, globals=0x2, locals=0xe64b9ca8, args=0x84bf63c, argcount=2, kws=0x84bf644, kwcount=0, defs=0xf59567d8, defcount=2, closure=0x0) at Python/ceval.c:2736 #11 0x080b23d2 in fast_function (func=0x2, pp_stack=0xffffa15c, n=2, na=-431252312, nk=0) at Python/ceval.c:3651 #12 0x080b1f3f in call_function (pp_stack=0xffffa15c, oparg=-431252312) at Python/ceval.c:3579 #13 0x080afebc in PyEval_EvalFrame (f=0x84bf4c4) at Python/ceval.c:2163 #14 0x080b2467 in fast_function (func=0x2, pp_stack=0xffffa2bc, n=1, na=-431252312, nk=0) at Python/ceval.c:3640 #15 0x080b1f3f in call_function (pp_stack=0xffffa2bc, oparg=-431252312) at Python/ceval.c:3579 #16 0x080afebc in PyEval_EvalFrame (f=0x84bd724) at Python/ceval.c:2163 #17 0x080b2467 in fast_function (func=0x2, pp_stack=0xffffa41c, n=2, na=-431252312, nk=0) at Python/ceval.c:3640 #18 0x080b1f3f in call_function (pp_stack=0xffffa41c, oparg=-431252312) at Python/ceval.c:3579 #19 0x080afebc in PyEval_EvalFrame (f=0x84b61d4) at Python/ceval.c:2163 #20 0x080b2467 in fast_function (func=0x2, pp_stack=0xffffa57c, n=3, na=-431252312, nk=0) at Python/ceval.c:3640 #21 0x080b1f3f in call_function (pp_stack=0xffffa57c, oparg=-431252312) at Python/ceval.c:3579 #22 0x080afebc in PyEval_EvalFrame (f=0x863040c) at Python/ceval.c:2163 #23 0x080b2467 in fast_function (func=0x2, pp_stack=0xffffa6dc, n=1, na=-431252312, nk=0) at Python/ceval.c:3640 #24 0x080b1f3f in call_function (pp_stack=0xffffa6dc, oparg=-431252312) at Python/ceval.c:3579 #25 0x080afebc in PyEval_EvalFrame (f=0x85f95a4) at Python/ceval.c:2163 #26 0x080b098e in PyEval_EvalCodeEx (co=0xf5888f20, globals=0x2, locals=0xe64b9ca8, args=0xf595d9f8, argcount=1, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:2736 #27 0x0810ee8a in function_call (func=0xf588eb1c, arg=0xf595d9ec, kw=0x0) at Objects/funcobject.c:548 #28 0x0805c807 in PyObject_Call (func=0x1, arg=0xe64b9ca8, kw=0xe64b9ca8) at Objects/abstract.c:1756 #29 0x080644fb in instancemethod_call (func=0xf588eb1c, arg=0xf595d9ec, kw=0xe64b9ca8) at Objects/classobject.c:2447 #30 0x0805c807 in PyObject_Call (func=0x1, arg=0xe64b9ca8, kw=0xe64b9ca8) at Objects/abstract.c:1756 #31 0x080b1cca in PyEval_CallObjectWithKeywords (func=0xe64b9ca8, arg=0xf7d1d02c, kw=0xf5894e64) at Python/ceval.c:3425 #32 0x080a6cc6 in builtin_apply (self=0x0, args=0xe64b9ca8) at Python/bltinmodule.c:100 #33 0x0810f4cd in PyCFunction_Call (func=0xf7d25dcc, arg=0x0, kw=0x1) at Objects/methodobject.c:108 #34 0x080b225e in call_function (pp_stack=0xffffabdc, oparg=-431252312) at Python/ceval.c:3558 #35 0x080afebc in PyEval_EvalFrame (f=0x8330d4c) at Python/ceval.c:2163 #36 0x080b098e in PyEval_EvalCodeEx (co=0xf676c8a0, globals=0x2, locals=0xe64b9ca8, args=0xf595dbd8, argcount=1, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:2736 #37 0x0810ee8a in function_call (func=0xf6713fb4, arg=0xf595dbcc, kw=0x0) at Objects/funcobject.c:548 #38 0x0805c807 in PyObject_Call (func=0x1, arg=0xe64b9ca8, kw=0xe64b9ca8) at Objects/abstract.c:1756 #39 0x080644fb in instancemethod_call (func=0xf6713fb4, arg=0xf595dbcc, kw=0xe64b9ca8) at Objects/classobject.c:2447 #40 0x0805c807 in PyObject_Call (func=0x1, arg=0xe64b9ca8, kw=0xe64b9ca8) at Objects/abstract.c:1756 #41 0x080b1cca in PyEval_CallObjectWithKeywords (func=0xe64b9ca8, arg=0xf7d1d02c, kw=0xf589d16c) at Python/ceval.c:3425 #42 0xf789a6ca in PythonCmd (clientData=0xf7d1d02c, interp=0x8337ae8, argc=1, argv=0xffffafe0) at /var/tmp/chimera-build/foreign/src/Python-2.4.2/Modules/_tkinter.c:1998 #43 0xf6bd2caf in TclInvokeStringCommand () from /usr/local/chimera/lib/libtcl8.4.so #44 0xf6bd3d34 in TclEvalObjvInternal () from /usr/local/chimera/lib/libtcl8.4.so #45 0xf6bfb59b in TclExecuteByteCode () from /usr/local/chimera/lib/libtcl8.4.so #46 0xf6bfaa73 in TclCompEvalObj () from /usr/local/chimera/lib/libtcl8.4.so #47 0xf6bd50a2 in Tcl_EvalObjEx () from /usr/local/chimera/lib/libtcl8.4.so #48 0xf6ca5d01 in TkInvokeButton () from /usr/local/chimera/lib/libtk8.4.so #49 0xf6ca4efa in ButtonWidgetObjCmd () from /usr/local/chimera/lib/libtk8.4.so #50 0xf6bd3d34 in TclEvalObjvInternal () from /usr/local/chimera/lib/libtcl8.4.so #51 0xf6bd40b4 in Tcl_EvalObjv () from /usr/local/chimera/lib/libtcl8.4.so #52 0xf6bd4fdc in Tcl_EvalObjEx () from /usr/local/chimera/lib/libtcl8.4.so #53 0xf6c2dcca in Tcl_UplevelObjCmd () from /usr/local/chimera/lib/libtcl8.4.so #54 0xf6bd3d34 in TclEvalObjvInternal () from /usr/local/chimera/lib/libtcl8.4.so #55 0xf6bfb59b in TclExecuteByteCode () from /usr/local/chimera/lib/libtcl8.4.so #56 0xf6bfaa73 in TclCompEvalObj () from /usr/local/chimera/lib/libtcl8.4.so #57 0xf6c2e3a7 in TclObjInterpProc () from /usr/local/chimera/lib/libtcl8.4.so #58 0xf6bd3d34 in TclEvalObjvInternal () from /usr/local/chimera/lib/libtcl8.4.so #59 0xf6bd4904 in Tcl_EvalEx () from /usr/local/chimera/lib/libtcl8.4.so #60 0xf6bd4dab in Tcl_Eval () from /usr/local/chimera/lib/libtcl8.4.so #61 0xf6bd6666 in Tcl_GlobalEval () from /usr/local/chimera/lib/libtcl8.4.so #62 0xf6c7934b in Tk_BindEvent () from /usr/local/chimera/lib/libtk8.4.so #63 0xf6c7f245 in TkBindEventProc () from /usr/local/chimera/lib/libtk8.4.so #64 0xf6c86d41 in Tk_HandleEvent () from /usr/local/chimera/lib/libtk8.4.so #65 0xf6c875f6 in WindowEventProc () from /usr/local/chimera/lib/libtk8.4.so #66 0xf6c23408 in Tcl_ServiceEvent () from /usr/local/chimera/lib/libtcl8.4.so #67 0xf6c236b6 in Tcl_DoOneEvent () from /usr/local/chimera/lib/libtcl8.4.so #68 0xf7898b24 in Tkapp_MainLoop (_self=0xf6b003a0, args=0xe64b9ca8) at /var/tmp/chimera-build/foreign/src/Python-2.4.2/Modules/_tkinter.c:2536 #69 0x0810f4cd in PyCFunction_Call (func=0xf5a1b2cc, arg=0xf6b003a0, kw=0x1) at Objects/methodobject.c:108 #70 0x080b225e in call_function (pp_stack=0xffffc4fc, oparg=-431252312) at Python/ceval.c:3558 #71 0x080afebc in PyEval_EvalFrame (f=0x8337914) at Python/ceval.c:2163 #72 0x080b098e in PyEval_EvalCodeEx (co=0xf6ddc1e0, globals=0x2, locals=0xe64b9ca8, args=0x833e1f4, argcount=1, kws=0x833e1f8, kwcount=0, defs=0xf6d5e6f8, defcount=1, closure=0x0) at Python/ceval.c:2736 #73 0x080b23d2 in fast_function (func=0x2, pp_stack=0xffffc6cc, n=1, na=-431252312, nk=0) at Python/ceval.c:3651 #74 0x080b1f3f in call_function (pp_stack=0xffffc6cc, oparg=-431252312) at Python/ceval.c:3579 #75 0x080afebc in PyEval_EvalFrame (f=0x833e0a4) at Python/ceval.c:2163 #76 0x080b2467 in fast_function (func=0x2, pp_stack=0xffffc82c, n=0, na=-431252312, nk=0) at Python/ceval.c:3640 #77 0x080b1f3f in call_function (pp_stack=0xffffc82c, oparg=-431252312) at Python/ceval.c:3579 #78 0x080afebc in PyEval_EvalFrame (f=0x818cf34) at Python/ceval.c:2163 #79 0x080b098e in PyEval_EvalCodeEx (co=0xf7ce09a0, globals=0x2, locals=0xe64b9ca8, args=0x818a5a4, argcount=1, kws=0x818a5a8, kwcount=0, defs=0xf7d5b8a8, defcount=12, closure=0x0) at Python/ceval.c:2736 #80 0x080b23d2 in fast_function (func=0x2, pp_stack=0xffffc9fc, n=1, na=-431252312, nk=0) at Python/ceval.c:3651 #81 0x080b1f3f in call_function (pp_stack=0xffffc9fc, oparg=-431252312) at Python/ceval.c:3579 #82 0x080afebc in PyEval_EvalFrame (f=0x818a454) at Python/ceval.c:2163 #83 0x080b098e in PyEval_EvalCodeEx (co=0xf7ce0620, globals=0x2, locals=0xe64b9ca8, args=0x0, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:2736 #84 0x080adc17 in PyEval_EvalCode (co=0xe64b9ca8, globals=0xe64b9ca8, locals=0xe64b9ca8) at Python/ceval.c:484 #85 0x080e4339 in run_node (n=0xf7d35824, filename=0xe64b9ca8 "", globals=0xe64b9ca8, locals=0xe64b9ca8, flags=0xe64b9ca8) at Python/pythonrun.c:1265 #86 0x080e3744 in PyRun_SimpleFileExFlags (fp=0x8153008, filename=0xffffd479 "/usr/local/chimera/share/__main__.py", closeit=1, flags=0xffffcbc4) at Python/pythonrun.c:860 #87 0x080e30fa in PyRun_AnyFileExFlags (fp=0x8153008, filename=0xffffd479 "/usr/local/chimera/share/__main__.py", closeit=1, flags=0xffffcbc4) at Python/pythonrun.c:664 #88 0x080559c6 in Py_Main (argc=1, argv=0xffffcc84) at Modules/main.c:484 #89 0x080553a9 in main (argc=-431252312, argv=0xe64b9ca8) at Modules/python.c:23 (gdb) quit

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Chimera-dev October 2006