- Chimera-dev - RBVI Mailing Lists

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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Re: [chimera-dev] [Chimera-users] Non-gui chimera in a shell?
by Eric Pettersen 09 May '06

09 May '06

What Tom says below is all true, but as he intimated in his previous mail if you are willing/able to use Chimera as your Python interpreter (typically as "chimera --nogui script.py") then things should work. There are some caveats. Chimera ignores the PYTHONPATH environment variable in order to avoid using libraries from incompatible Python installations, therefore to have Chimera find locally installed packages that you want to use you need to set the CHIMERAPATH variable, which Chimera uses in a fashion similar to PYTHONPATH. Another thing is that you can't pass arguments to your script in the conventional fashion since Chimera itself processes all arguments. If you need to pass values to your script, you need to use environment variables as detailed in the FAQ here: http:// www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3 --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu On May 8, 2006, at 9:27 PM, Thomas Goddard wrote: > Hi Jim, > > Importing Chimera from your Python script to use its > functionality is > something we have put very little effort into supporting. I have done > this in an nuclear magnetic resonance assignment program called Sparky > that is based on Python to run Chimera as a structure viewer. > Below is > the code that starts Chimera from the Sparky Python interpretter. > > There are many problems. > > You need to set an environment variable to tell the operating system > where the Chimera shared libraries are before you start Python. See > example below. > > You need to use the Python included with Chimera because Chimera > uses a modified Python. Ick. The modification allows Chimera objects > like Molecules to be given new attributes. There is also some other > issue on the Mac where a stock Python can't find the init_chimera() > method in shared library _chimera.so. > > If you start the Chimera graphical user interface then you will need > to run the Tk event-loop to get Chimera to update the graphics. But > then Chimera will not return to your script that started it. So my > example below does not start the event-loop. > > If you start Chimera in nogui mode, it quits as soon as it processes > any arguments which would probably prevent your script from calling > into > Chimera after that as Chimera has cleaned up. > > When I used the script below and then opened a PDB file on my Mac OS > 10.4.6 system the screen went dim and a message told me to hold the > power button down to do a hard reboot! Probably a graphics driver > issue. > > As you can see we really haven't worked much on this type of > Chimera use. > > Tom > > ---- > > Example starting Chimera on a Mac from Python: > > $ export CHIMERA="/Users/goddard/Desktop/Chimera 2199.app/Contents/ > Resources" > $ export DYLD_LIBRARY_PATH=$CHIMERA/lib > $ "/Users/goddard/Desktop/Chimera 2199.app/Contents/Resources/bin/ > python2.4" > Python 2.4.2 (#1, Jan 30 2006, 11:15:23) > [GCC 4.0.1 (Apple Computer, Inc. build 5247)] on darwin > Type "help", "copyright", "credits" or "license" for more information. >>>> import start_chimera >>>> start_chimera.start_chimera() >>>> >>>> # Now you could "import chimera" and do some stuff. >>>> > > --- > > The following is the start_sparky.py file used in the above example: > > # > ---------------------------------------------------------------------- > ------- > # > start_count = 0 > def start_chimera(): > > setup_chimera() > > import chimeraInit > try: > chimeraInit.init(argv = [], nogui = False, eventloop = False, > exitonquit = False) > except SystemExit, value: > # Chimera raises SystemExit sometimes when it can't start. > # Have to catch it here or Sparky will exit. > import traceback > traceback.print_exc() > raise EnvironmentError, 'Chimera failed to start' > except: > global start_count > if start_count == 1: > warning = ''' > Chimera can only be started once per Sparky session. > This is a limitation in all versions of Chimera released so far > (through March 2004). > > ''' > import sys > sys.stdout.write(warning) > raise > > start_count += 1 > > # > ---------------------------------------------------------------------- > ------- > # Do initial Chimera setup that only needs to be done once even if > Chimera > # is started and quit several times. > # > chimera_setup = False > def setup_chimera(): > > global chimera_setup > if chimera_setup: > return > chimera_setup = True > > import os > if not os.environ.has_key('CHIMERA'): > raise EnvironmentError, 'CHIMERA environment variable not set.' > > chimera_path = os.environ['CHIMERA'] > import os.path > if not os.path.exists(chimera_path): > raise EnvironmentError, 'CHIMERA environment variable gives non- > existent directory ' + chimera_path > > chimera_python = os.path.join(chimera_path, 'share') > chimera_lib = os.path.join(chimera_path, 'lib') > import sys > if sys.platform == 'win32': > chimera_site_packages = os.path.join(chimera_path, 'bin', 'Lib', > 'site-packages') > else: > chimera_site_packages = os.path.join(chimera_path, 'lib', > 'python2.4', > 'site-packages') > > sys.path.insert(0, chimera_site_packages) > sys.path.insert(0, chimera_python) > sys.path.insert(0, chimera_lib) > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Benchmark results
by Daniil Zaitsev 24 Apr '06

24 Apr '06

Graphics ATI Mobility Radeon X1300 Processor Intel Core Duo T2300 Clock (MHz) 1700 OS Type Windows XP Media Edition Surface 394 Mesh 486 Contour 141 Solid 256 Recolor 88 Notes Laptop Test Date 4/06 Chimera Version 1.2199 Machine Dell Inspiron E1505 (laptop) Graphics Memory (Mb) 128 Main Memory (Mb) 512 OS Version Windows XP Media Edition Driver Version Host name

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for Eric Petterson
by Bill Gleason 17 Apr '06

17 Apr '06

Hi Eric, Could you please reply to this directly so that I have your email address? Couldn't find the "direct mail address." We are having some weird problems with reopening the .py session files. Can't really put a finger on it, but every once in a while a .py file gets written and it cannot be opened by Chimera. Not all the time, mostly it is ok, but it can be really annoying when it happens. We are running (mostly) Windows although also some Linux boxes. I can't really remember this happening on Linux. Thanks for any comments. Bill -- William B. Gleason, University of Minnesota Associate Professor, Department of Laboratory Medicine & Pathology Fellow, University of Minnesota Supercomputer Institute Graduate Faculty: Chemistry, Medicinal Chemistry, and Biomedical Engineering (612) 626-2455 (office) (612) 626-5115 (lab) www.umn.edu/~bgleason

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Re: [chimera-dev] [Chimera-users] Rotation about an axis
by Thomas Goddard 11 Apr '06

11 Apr '06

Hi Jordan, I see one mistake in your code, related to a confusing aspect of Chimera transform objects. mvo = apply(chimera.Vector, origin) vo = ref_model.openState.xform.apply(mvo) Here you use Xform.apply(Vector). Xform is a rotation and a translation but when applied to a Vector you get only the rotation applied. That is what you want if you are reorienting an axis, but not if you are repositioning the origin. The Xform.apply(Point) method applies both the rotation and translation. So you want: mvo = apply(chimera.Point, origin) vo = ref_model.openState.xform.apply(mvo) In fact, that apply() call is old style Python and I would use: mvo = chimera.Point(*origin) vo = ref_model.openState.xform.apply(mvo) The * in front of the argument means each element of the sequence origin is passed as a separate argument. This change messes up the translate() lines further down: xf.translate(vo) xf.rotate(va, angle_deg) xf.translate(-vo) The Xform.translate(Vector) requires a Vector argument not a Point. So I'd change that to use Xform.translate(x,y,z) as follows xf.translate(vo.x, vo.y, vo.z) xf.rotate(va, angle_deg) xf.translate(-vo.x, -vo.y, -vo.z) An important detail to note is that the transform xf when applied to a point first translates by -vo, then rotates, the translates by +vo. That is the order is backwards from the above function calls that created the transform. (In the ContrainedMove code there is an incorrect comment about translate(u) actually translating by -u -- I didn't realize what was going on when I wrote that code.) If I understand your code correctly you are specifying a line (origin and axis) to rotate about in the coordinate system of ref_model, then expressing that line in Chimera global coordinates, and then rotating the second model about that line. There are so many pits to fall into with the Xform / Vector / Point Chimera code. And there is not documentation for it, other than reading the source code. This is especially excruciating because it is hard to even find the source code. I looked at Chimera source code file chimera/libs/_chimera/pyinterface to see the Python interface to the C++ Xform, Vector, and Point objects. And then when I needed to actually look at the Xform C++ code I found that in otf/lib/geom3d/Xform.cpp which is in the Chimera foreign source code distribution (200 Mb) in a tar ball: chimera/foreign/otf/otf.tar.gz This source code is available from the Chimera web site. Could we make it any more difficult for you? It's a shameful mess. Feel free to ask further questions. There is a Chimera developers mailing list chimera-dev(a)cgl.ucsf.edu that is more appropriate for coding questions. Tom

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new chimera.fileInfo.register interface
by Greg Couch 08 Mar '06

08 Mar '06

There are now two additional keyword arguments to chimera.fileInfo.register: category and dangerous. The category should be set to one of the built-in categories or one you invent. The categories are meant to help organize all of the file types chimera can open. A set of default categories has been created, chimera.FileInfo.X where X is DYNAMICS for a molecular trajectory (amber), GENERIC3D for generic 3D objects (vrml, bild), SCRIPT for command scripts (python, midas), SEQUENCE for molecular sequences, STRUCTURE for molecule structure (pdb, mol2), SURFACE for molecular surfaces (grasp), and VOLUME for volume data. The dangerous flag defaults to True for scripts and false otherwise. You can override that default by giving the keyword. So far, the categories have only been added to the default file types in the chimera module and to the Midas module. Please update your uses of chimera.fileInfo.register in the extensions you maintain. - Greg

2 1

chimera.widgets.ModelOptionMenu aggressiveness
by Charlie Moad 06 Mar '06

06 Mar '06

I am using chimera.widgets.ModelOptionMenu in my plugin as suggested, but when I attempt to save a screen image its as if my plugin/the structure is being unmapped then mapped again. The tiles are rendered before my plugin reloads the interface. Is there a way I can programmatically destroy my plugin's instance so I can at least take a screenshot without anything changing? I poked around chimera.extension.manager without success. Thanks, Charlie

2 1

1.2199 and BILD
by Charlie Moad 28 Feb '06

28 Feb '06

First of all, sorry for posting all those extension questions on the user list. I just discovered the dev list. Could I get the headers needed for 1.2199 for linux and possibly OS10.4? I am wanting to make use of the BILD format and I have a few questions. If I generate a lot of polygons how efficient will it be, or is there some way to specify poly-strips/triangle-fans. Pertaining to PDB's as well, is there a way to open a file from a stream/string? I despise temp files. It would be nice to use a StringIO object to write my contents to, or do something like "chimera.openModels.openBuffer(myBuffer, type='PDB')", where myBuffer is anything with a read() method or maybe just a string. Thanks, - Charlie

4 4

publish collaboratory idl files?
by David E. Konerding 03 Feb '06

03 Feb '06

Hi Chimera developers, I was wondering if it would be possible to publish the Collaboratory IDL files? I would like to make a remote control application for chimera, but don't want to use the puppet extension. It seems like a nice way to do this would be to use the Collaboratory interface. Thanks, Dave

2 3

Fwd: Re: Tkinter_Idle askyesno issue
by Wolf Cochrane 13 Jan '06

13 Jan '06

My local Chimera python is Python2.3, and it works fine when I run the file with it. It is only when I run the file through the Chimera Idle version that it doesn't work. Wolf ----- Forwarded message from Conrad Huang <conrad(a)cgl.ucsf.edu> ----- Date: Thu, 12 Jan 2006 09:14:04 -0800 From: Conrad Huang <conrad(a)cgl.ucsf.edu> Reply-To: Conrad Huang <conrad(a)cgl.ucsf.edu> Subject: Re: [chimera-dev] Tkinter_Idle askyesno issue To: Wolf Cochrane <s24449424(a)tuks.co.za> Can you please try the same thing with Chimera's version of Python? It's in $CHIMERA/bin/python2.4, where $CHIMERA is where you installed Chimera. Thanks, Conrad On Jan 12, 2006, at 12:01 AM, Wolf Cochrane wrote: > Hi, > > I still have the same bug. The same file works fine if I run it > with my local > version of Python(on Suse 9.2), but when run through the Chimera > Idle version it > always returns "False". > > > > #------------------------------------------------------ > import Tkinter > import tkMessageBox > > print tkMessageBox.askyesno("Dialog","Click Yes or No") > > #------------------------------------------------------ > > > cheers > Wolf Cochrane > > > > > > > > > > > > > > tried this on Chimera 1.2184 on a Windows XP system and the code > returns True when you click Yes and False when you click No. > > Conrad > > On Jan 11, 2006, at 8:45 AM, Wolf Cochrane wrote: > >> Hi >> >> Is it just me of does this bit of code always print "False" when > >> run through >> Idle (Chimera v1.2065). If so, how to I get around it without >> having to build my >> own dialogs. >> >> >> >> import Tkinter >> import tkMessageBox >> >> #root = Tk() >> #root.geometry("500x510") >> #root.title("Yes/No") >> >> #root.mainloop() >> >> >> print tkMessageBox.askyesno("Linker range","Click Yes if a > range of >> Linkers will >> be used at this Permutation Site") >> >> >> >> >> Thanks >> Wolf >> >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev ----- End forwarded message -----

1 0

Re: [chimera-dev] Tkinter_Idle askyesno issue
by Wolf Cochrane 12 Jan '06

12 Jan '06

Hi, I still have the same bug. The same file works fine if I run it with my local version of Python(on Suse 9.2), but when run through the Chimera Idle version it always returns "False". #------------------------------------------------------ import Tkinter import tkMessageBox print tkMessageBox.askyesno("Dialog","Click Yes or No") #------------------------------------------------------ cheers Wolf Cochrane tried this on Chimera 1.2184 on a Windows XP system and the code returns True when you click Yes and False when you click No. Conrad On Jan 11, 2006, at 8:45 AM, Wolf Cochrane wrote: > Hi > > Is it just me of does this bit of code always print "False" when > run through > Idle (Chimera v1.2065). If so, how to I get around it without > having to build my > own dialogs. > > > > import Tkinter > import tkMessageBox > > #root = Tk() > #root.geometry("500x510") > #root.title("Yes/No") > > #root.mainloop() > > > print tkMessageBox.askyesno("Linker range","Click Yes if a range of > Linkers will > be used at this Permutation Site") > > > > > Thanks > Wolf > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

2 1

Tkinter_Idle askyesno issue
by Wolf Cochrane 11 Jan '06

11 Jan '06

Hi Is it just me of does this bit of code always print "False" when run through Idle (Chimera v1.2065). If so, how to I get around it without having to build my own dialogs. import Tkinter import tkMessageBox #root = Tk() #root.geometry("500x510") #root.title("Yes/No") #root.mainloop() print tkMessageBox.askyesno("Linker range","Click Yes if a range of Linkers will be used at this Permutation Site") Thanks Wolf

3 2

Concerns regarding secondary structure
by rquiroga＠immf.uncor.edu 08 Dec '05

08 Dec '05

Greetings, I have some concerns with Chimera's secondary structure detection/depiction. I am using Modeller to predict some 3D structures. I open my predicted structure in pdb file in Chimera along with the original structure I based my prediction on, and find that my predicted structure lacks two beta sheets that the model protein has, though the AA that compose the B-sheet are identical for the two proteins when I compare sequences with Matchmaker. I tried opening my predicted structure in MolMol and it detects the B-sheet, though I hugely prefer Chimera, so if you could solve this problem for me I would be very greatful. Thanks in advance, and regards Rodrigo Quiroga

1 0

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: 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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 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

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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

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benchmark results
by Boaz Shaanan 24 Oct '05

24 Oct '05

Hi, Since this subject came up I was tempted and ran it on my laptop (XP side; later on I'll try it on the linux side of the same laptop). So, here goes: Compaq Evo N800V, P4 1.6 Ghz, 512 Mb RAM, Radeon Mobility 7500, 32Mb memory on graphics card. Benchmark scores surface 119 mesh 122 contour 110 solid 99 recolor 63 Best regards, Boaz -- Boaz Shaanan, Ph.D. Associate Prof. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail:bshaanan@bgu.ac.il Phone:972-8-647-2220 Fax: 972-8-647-2992/646-1710

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benchmark
by Boaz Shaanan 22 Oct '05

22 Oct '05

Oops, I forgot: the chimera version is 2172 for Xp. Boaz -- Boaz Shaanan, Ph.D. Associate Prof. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail:bshaanan@bgu.ac.il Phone:972-8-647-2220 Fax: 972-8-647-2992/646-1710

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