- Chimera-dev - RBVI Mailing Lists

opening models
by Eric Pettersen 15 Dec '06

15 Dec '06

On Dec 15, 2006, at 1:07 PM, Randy Heiland wrote: > Eric, > Need a bit more help on this... how can I invoke this reader > programmatically from my plugin and display the model in the viewer > window? Til now, with PDB formatted files, I've done: > > fp = open(tmpfile.name, 'w') > fp.write(pdbstr) > fp.close() > self.model = chimera.openModels.open(tmpfile.name, type='PDB', > identifyAs=id[0]) If your temp file's name ends in '.sdf' then you don't have to supply a 'type' keyword to openModels.open(). If not, then with the code I gave you the 'type' would be "Structure Data Format" (it's the "fileType" variable in ReadSDF/fileInfo.py). You might want to import that variable and use it instead of a fixed string, because in the next release of Chimera the string will be "MDL MOL/SDF" since I enhanced the reader to handle MOL files as well. Also, openModels.open() always returns a _list_ of models, even if the input only creates one model. > Now I have a 'pdbstr' that's really an sdf format, and when I try to > substitue type='PDB' w/ 'SDF', it doesn't recognize it. > > And when I try the following, it doesn't complain, however no model is > displayed: > import ReadSDF > > fp = open(tmpfile.name, 'w') > fp.write(sdfstr) > fp.close() > self.model = ReadSDF.readSDF(tmpfile.name) The readSDF() function returns a list of models. To add them to the list of open models, use chimera.openModels.add(), probably like this: self.models = ReadSDF.readSDF(tmpfile.name) chimera.openModels.add(self.models) --Eric

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Re: [chimera-dev] C/C++ libraries in Chimera
by Elaine Meng 06 Dec '06

06 Dec '06

Hi Viktor, Actually, I'm the one person on the Chimera team that doesn't do programming! I'll share your mail with the chimera-dev(a)cgl.ucsf.edu list (for programmer/developer issues) - I believe it has a handful of subscribers in addition to the Chimera team members, and this set of people may have some valuable insights. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 6, 2006, at 9:28 AM, Viktor Hornak wrote: > Dear Elaine, > > sorry to write directly to you and not to chimera list but I have a > question which is rather off-topic. It concerns developing C > extensions in Python, and I don't even mean specifically for > chimera (at this time), but in general. I know that you guys (I am > not sure who specifically on chimera team does this sort of a "hard > core" programming work) develop a lot of extensions (.so libraries) > that can be called from Python and thus you must have a lot of > experience doing it. I attempted a couple times to write C > extensions in Python as described in Python extension guide but > always got burned by reference counting, programs crashing at > allocating memory or releasing pointers, etc. In other words, there > must be a better/easier way to write extensions. All I need is to > transfer integer/float variables and arrays to or from Python to my > C subroutine, e.g. I just need to wrap my existing C subroutines > and pass arrays back and forth between C and Python (I guess Python > lists versus C arrays). I was hoping someone on your team could > point me to the right direction. I saw people use SWIG (that looked > rather complex though and an overkill for what I need), or Pyrex, > etc but I wasn't sure which solution was worth picking up in terms > of time I have to spend to learn it and future support (so that the > project doesn't disappear in a year). > I would really appreciate if you could provide any hints or point > me to some resources. > > Many thanks for your help and sorry for such an unrelated question!!! > > Cheers, > -Viktor > > -- > =================================================================== > Viktor Hornak > Center for Structural Biology Phone: (631)632-1439 > SUNY at Stony Brook Fax: (631)632-1555 > Stony Brook, NY 11794-5115 E-mail: viktor.hornak(a)sunysb.edu > ===================================================================

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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 help
by Vishal Pua 28 Sep '06

28 Sep '06

Hi, I was wondering if there was a way to create a script, that would open pdb files, render them to look a certain way ex. wire or ribbon, then save, automatically? this would have to work for a number of pdb files? I have little programming experience, and wonder if there was an easy way to do this, thanks Vishal Pua

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post to the list
by Javier Díez 25 Sep '06

25 Sep '06

I would like to post to this list. chimera-dev(a)cgl.ucsf.edu Thanks

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Chimera question
by Thomas Goddard 21 Aug '06

21 Aug '06

Hi Sangeetha, If you want to run Chimera you should get one of the compiled distributions on the download page: http://www.cgl.ucsf.edu/chimera/download.html The source code you downloaded is for Chimera developers who are developing additional Chimera tools. It does not include executables and it is not simple to produce executables from the source code. Tom

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Chimera :installation problem
by sangeetha 18 Aug '06

18 Aug '06

Hi, I get the following error when i installed chimera-1.2199-source.tar.gz in Linux and tried to run chimera. Please help # ./chimera ./chimera: line 160: exec: python2.4: not found Thanks sangeetha S.Sangeetha Research Assistant, C/o Dr.Dinesh Gupta, Structural and Computational Biology, International Center for Genetic Engineering and Biotechnology, Aruna asaf ali marg, NewDelhi-110067 Mobile : +91 98910 64332 Web : http://www.icgeb.org

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