- Chimera-users - RBVI Mailing Lists

Fwd: longbond and session restore problems
by Elaine Meng 14 Nov '06

14 Nov '06

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: November 14, 2006 10:36:35 AM PST > To: jean-francois menetret <menetret(a)bu.edu> > Cc: Eric Pettersen <pett(a)cgl.ucsf.edu>, Thomas Goddard > <goddard(a)cgl.ucsf.edu>, Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] longbond and session restore problems > > Hi Jean-Francois, > In my tests I didn't have this problem; showing Pipes-and-Planks > should not change which atoms and bonds are shown. > > However, I might understand what is happening: when you show the > "chain trace" of CA atoms only, a connection across the missing > part is shown even after you use "~longbond". This CA connection > line is different than the "missing segments" pseudobonds: > > -CA-CA-------CA-CA- > is the chain trace, not affected by ~longbond > > -N-CA-C- - - -N-CA-C- > is the backbone showing "real bonds" except for the pseudobond, > which is affected by ~longbond > > If you are showing just the CA atoms and you don't want the > connection, here are some possibilities: > (1) just hide all the CA atoms (for example, command: ~disp @ca) > OR > (2) change from "chain trace" (the CA atoms) to "backbone > only" (N,CA,C) - if you used ~longbond the connection will be gone > OR > (3) if you really wanted to keep showing just the CA atoms, you can > select each long CA-CA bond (which is also a pseudobond, although > not shown with a dashed line) with Ctrl-click, and use the > Selection Inspector to undisplay it. This tool is opened by > clicking the button on the lower right of the Chimera window. In > the Inspector, change to Inspect [Pseudobond] and change the > "displayed" attribute to "false." > > I hope this helps, > Elaine > > On Nov 14, 2006, at 6:51 AM, jean-francois menetret wrote: > >> Hi Elaine, >> >> thank you for your message >> I still have one problem with the long bonds, though : there >> reappear in pipes-and-plancks. >> About restoring a session, I agree, it was not an issue with the >> chimera version but with the speed/memory of my PC. Although >> chimera could save the session, it couldn't reopen it on my PC but >> it did on a faster one. >> >> Best wishes >> >> Jean-François Ménétret, PhD >> Boston University School of Medicine >> Physiology and Biophysics Department >> 700 Albany Street W315 >> Boston, MA 02118 >> Email: menetret(a)bu.edu >> Mailing address: 715 Albany Street > > ----- > 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 >

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longbond and session restore problems
by Thomas Goddard 09 Nov '06

09 Nov '06

Here are two problems reported by Jean-Francois Menetret in Chimera 2304 and 2306. ------- Start of forwarded message ------- Date: Thu, 9 Nov 2006 16:38:58 -0500 (EST) From: jean-francois menetret <menetret(a)bu.edu> To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: problems report Hi Thomas, I have two problems to report 1) the longbond command doesn't seem to work (with chimera 2304 or 2306) 2) I saved a session under chimera 2304 but couldn't open it after=20 upgrading to 2306 Jean-Francois Jean-Fran=E7ois M=E9n=E9tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street ------- End of forwarded message -------

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Re: [Chimera-users] Fwd: Chimera crashes with MacPro show solid
by Thomas Goddard 09 Nov '06

09 Nov '06

Peter EngelHardt replies about solid rendering crash on Mac. ------- Start of forwarded message ------- Date: Thu, 9 Nov 2006 22:42:41 +0300 To: Thomas Goddard <goddard(a)cgl.ucsf.edu> From: Peter Engelhardt <engelhar(a)medi.mappi.helsinki.fi> Subject: Re: [Chimera-users] Fwd: Chimera crashes with MacPro show solid Dear Tom, Thanks, I did what you told and it all worked out very fine Though a bit buggy - volumes disappear and appear suddenly - but under certain control anyhow. Cheers and thanks again Peter > The crash with solid rendering is almost surely a graphics driver bug. >The solid rendering code works correctly on many different graphics cards >and there is nothing in that code that works differently for stereo >rendering. > > Does the crash occur for solid rendering without stereo? yes instantly > > Does the size of the data set matter? not tested > > There are two solid rendering options that may avoid this crash. >These are shown in the volume dialog using the Features / Solid Rendering >Options menu entry. From the back trace you sent I see the crash occurs >when pushing the data to the graphics card and mapping the colors using >a colormap. If you turn off the option "Use colormap of size X for solids" >then different code will be used -- colors will be computed on the CPU >instead of on the graphics card. A second change that may avoid the >crash is turning off "Solids using 2D textures". This makes Chimera use >3 dimensional textures instead of 2 dimensional textures. > > Tom - -- ___________________________________________________________ Peter Engelhardt, PhD, docent Assistant Professor in Molecular Genetics Unit of Molecular Electron Tomography Department of Pathology and Virology Haartman Institute P.O.Box 21, FI-00014 Univ. of Helsinki, Finland Visiting Address: Haartmaninkatu 3, Helsinki ------- End of forwarded message -------

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Fwd: Chimera crashes with MacPro show solid
by Peter Engelhardt 09 Nov '06

09 Nov '06

In our Mac Pro Quad-Core 2.66GHz CTO Processor: 2.66 GHz Quad Xeon RAM 4G and NVIDIA Quadro FX 4500 512MB SDRAM, using Crystal Eyes Stereo Stereo works with iso surface and mesh but: CRASHES with show solid? Peter PS Following errors were reported and fwd to apple. >Date/Time: 2006-11-07 17:17:49.047 +0200 >OS Version: 10.4.8 (Build 8L2127) >Report Version: 4 > >Command: python2.4 >Path: /Applications/Chimera.app/Contents/Resources/bin/python2.4 >Parent: WindowServer [55] > >Version: 1.2303 (1.2303) > >PID: 457 >Thread: 0 > >Exception: EXC_BAD_ACCESS (0x0001) >Codes: KERN_PROTECTION_FAILURE (0x0002) at 0x000000a4 > >Thread 0 Crashed: >0 libGLImage.dylib 0x940a3fc4 glgProcessColor(GLDPixelMode >const*, GLGOperation const*, unsigned long) + 46870 >1 libGLImage.dylib 0x940972aa glgProcessPixels + 296 >2 com.apple.GeForceFXGLDriver 0x028b4f1e gldGetTextureLevel + 10243 >3 GLEngine 0x02732062 glTexSubImage2D_Exec + 1633 >4 libGL.dylib 0x92b0edaa glTexSubImage2D + 139 >5 _volume.so 0x037fb30f Texture_2d::fill(unsigned >short*) + 147 >6 _volume.so > 0x037fb424 Texture_Plane::fill_texture() >+ 76 >7 _volume.so 0x037fb627 >Volume_Renderer_2DT::update_colormap_textures(int) + 159 >8 _volume.so 0x037fd865 >Volume_Renderer_2DT::update_texture_planes(int) + 567 >9 _volume.so > 0x037fd9d8 Volume_Renderer_2DT::draw() + >122 >10 _chimera.dylib > 0x0101c5f8 chimera::LensModel::xformDraw >(chimera::LensViewer const*, chimera::LensViewer::DrawPass) const + 572 >11 _chimera.dylib 0x010190e1 chimera::Lens::draw >(chimera::LensViewer const*, chimera::LensViewer::DrawPass, int const*) + >241 >12 _chimera.dylib 0x01020e98 >chimera::LensViewer::drawScreenBoxes(otf::Array<int, (unsigned long)4> >const&, __gnu_cxx::__normal_iterator<chimera::ScreenBox*, >std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >, >__gnu_cxx::__normal_iterator<chimera::ScreenBox*, >std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >) >const + 1024 >13 _chimera.dylib 0x01022674 chimera::LensViewer::draw >(bool) const + 460 >14 _chimera.dylib > 0x0101dd34 chimera::LensViewer::displayCB >(_object*) + 90 >15 _chimera.dylib 0x01095323 LensViewer_displayCB + 43 >16 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >17 python2.4 > 0x0005d0ee PyEval_CallObjectWithKeywords >+ 112 (ceval.c:3430) >18 python2.4 0x000b89dc builtin_apply + 201 >(bltinmodule.c:100) >19 python2.4 0x0006359e PyEval_EvalFrame + 22313 >(ceval.c:3563) >20 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >21 python2.4 0x000b6570 function_call + 320 >(funcobject.c:548) >22 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >23 python2.4 0x0000c662 instancemethod_call + 401 >(classobject.c:2447) >24 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >25 python2.4 > 0x0005d0ee PyEval_CallObjectWithKeywords >+ 112 (ceval.c:3430) >26 _tkinter.so 0x016efea4 PythonCmd + 220 (_tkinter.c: >2001) >27 libtcl8.4.dylib 0x0a00d10f TclInvokeStringCommand + 121 >28 libtcl8.4.dylib 0x0a00fa41 TclEvalObjvInternal + 769 >29 libtcl8.4.dylib 0x0a010694 Tcl_EvalObjv + 232 >30 libTogl2.0.dylib 0x0255d047 Togl_CallCallback + 144 >31 libTogl2.0.dylib 0x0255d235 Togl_Render + 46 >32 libtcl8.4.dylib 0x0a0648a9 TclServiceIdle + 65 >33 libtcl8.4.dylib 0x0a055661 Tcl_DoOneEvent + 380 >34 libtk8.4.dylib 0x0b00ae3a Tk_UpdateObjCmd + 44 >35 libtcl8.4.dylib 0x0a00fa41 TclEvalObjvInternal + 769 >36 libtcl8.4.dylib 0x0a010694 Tcl_EvalObjv + 232 >37 _tkinter.so > 0x016f18ad Tkapp_Call + 199 (_tkinter.c: >1314) >38 python2.4 0x0006359e PyEval_EvalFrame + 22313 >(ceval.c:3563) >39 python2.4 0x000638b1 PyEval_EvalFrame + 23100 >(ceval.c:3645) >40 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >41 python2.4 0x0006370c PyEval_EvalFrame + 22679 >(ceval.c:3656) >42 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >43 python2.4 0x000b6570 function_call + 320 >(funcobject.c:548) >44 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >45 python2.4 0x000617c2 PyEval_EvalFrame + 14669 >(ceval.c:3840) >46 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >47 python2.4 0x000b6570 function_call + 320 >(funcobject.c:548) >48 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >49 python2.4 > 0x0005d0ee PyEval_CallObjectWithKeywords >+ 112 (ceval.c:3430) >50 python2.4 0x000b89dc builtin_apply + 201 >(bltinmodule.c:100) >51 python2.4 0x0006359e PyEval_EvalFrame + 22313 >(ceval.c:3563) >52 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >53 python2.4 0x000b6570 function_call + 320 >(funcobject.c:548) >54 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >55 python2.4 0x0000c662 instancemethod_call + 401 >(classobject.c:2447) >56 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >57 python2.4 > 0x0005d0ee PyEval_CallObjectWithKeywords >+ 112 (ceval.c:3430) >58 _tkinter.so 0x016efea4 PythonCmd + 220 (_tkinter.c: >2001) >59 libtcl8.4.dylib 0x0a00d10f TclInvokeStringCommand + 121 >60 libtcl8.4.dylib 0x0a00fa41 TclEvalObjvInternal + 769 >61 libtcl8.4.dylib 0x0a00fd57 Tcl_EvalEx + 503 >62 libtcl8.4.dylib 0x0a064f95 AfterProc + 106 >63 libtcl8.4.dylib 0x0a06477b TimerHandlerEventProc + 94 >64 libtcl8.4.dylib 0x0a055366 Tcl_ServiceEvent + 131 >65 libtcl8.4.dylib 0x0a05558f Tcl_DoOneEvent + 170 >66 _tkinter.so 0x016ef69f Tkapp_MainLoop + 188 >(_tkinter.c:2539) >67 python2.4 0x0006359e PyEval_EvalFrame + 22313 >(ceval.c:3563) >68 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >69 python2.4 0x0006370c PyEval_EvalFrame + 22679 >(ceval.c:3656) >70 python2.4 0x000638b1 PyEval_EvalFrame + 23100 >(ceval.c:3645) >71 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >72 python2.4 0x0006370c PyEval_EvalFrame + 22679 >(ceval.c:3656) >73 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >74 python2.4 > 0x0006450a PyEval_EvalCode + 87 (ceval.c: >490) >75 python2.4 0x0008af5c PyRun_FileExFlags + 200 >(pythonrun.c:1265) >76 python2.4 > 0x0008b23f PyRun_SimpleFileExFlags + 640 >(pythonrun.c:860) >77 python2.4 0x00005974 Py_Main + 3199 (main.c:493) >78 python2.4 0x00001cc6 _start + 216 >79 python2.4 0x00001bed start + 41 > >Thread 1: >0 libSystem.B.dylib 0x90019d3c select + 12 >1 libSystem.B.dylib 0x90023d87 _pthread_body + 84 > >Thread 0 crashed with X86 Thread State (32-bit): > eax: 0x00000002 ebx: 0x940988bf ecx: 0x00000000 edx: 0x00000001 > edi: 0x00000000 esi: 0x608d1000 ebp: 0xbfffba68 esp: 0xbfffb720 > ss: 0x0000001f efl: 0x00010246 eip: 0x940a3fc4 cs: 0x00000017 > ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 > >Binary Images Description: > 0x1000 - 0xd2fff python2.4 /Applications/Chimera.app/Contents/ >Resources/bin/python2.4 > 0x392000 - 0x394fff libtr.dylib /Applications/Chimera.app/Contents/ >Resources/lib/libtr.dylib > 0x3d8000 - 0x3dafff operator.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/operator.so > 0x3e4000 - 0x3e4fff _weakref.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_weakref.so > 0x3f0000 - 0x3f0fff _chimera.so /Applications/Chimera.app/Contents/ >Resources/lib/_chimera.so > 0x3f9000 - 0x3fbfff libwrappy2.dylib /Applications/Chimera.app/ >Contents/Resources/lib/libwrappy2.dylib > 0x505000 - 0x585fff libotf.dylib /Applications/Chimera.app/Contents/ >Resources/lib/libotf.dylib > 0x5a8000 - 0x5b0fff libXext.6.dylib /usr/X11R6/lib/libXext.6.dylib > 0x5cd000 - 0x5ddfff libz.dylib /Applications/Chimera.app/Contents/ >Resources/lib/libz.dylib > 0x5e5000 - 0x5e8fff strop.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/strop.so > 0x5f5000 - 0x5f6fff MacOS.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/MacOS.so > 0x705000 - 0x711fff libftgl.dylib /Applications/Chimera.app/Contents/ >Resources/lib/libftgl.dylib > 0x1008000 - 0x11b5fff _chimera.dylib /Applications/Chimera.app/ >Contents/Resources/lib/_chimera.dylib > 0x1300000 - 0x1340fff libfreetype.6.dylib > /Applications/Chimera.app/Contents/Resources/lib/libfreetype.6.dylib > 0x148b000 - 0x14e6fff libGLU.1.dylib /usr/X11R6/lib/libGLU.1.dylib > 0x1511000 - 0x156bfff libGL.1.dylib /usr/X11R6/lib/libGL.1.dylib > 0x159f000 - 0x165cfff libX11.6.dylib /usr/X11R6/lib/libX11.6.dylib > 0x1684000 - 0x16bcfff _vrml.so /Applications/Chimera.app/Contents/ >Resources/lib/_vrml.so > 0x16ec000 - 0x16f2fff _tkinter.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_tkinter.so > 0x1707000 - 0x1708fff math.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/math.so > 0x1710000 - 0x1711fff _random.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_random.so > 0x17f9000 - 0x17f9fff _imagingtk.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/PIL/_imagingtk.so > 0x2048000 - 0x204afff binascii.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/binascii.so > 0x2054000 - 0x2055fff fcntl.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/fcntl.so > 0x205d000 - 0x20a1fff _imaging.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/PIL/_imaging.so > 0x2133000 - 0x2136fff array.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/array.so > 0x2176000 - 0x2177fff _ssl.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_ssl.so > 0x220f000 - 0x2215fff _socket.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_socket.so > 0x222a000 - 0x222bfff time.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/time.so > 0x2275000 - 0x2276fff cStringIO.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/cStringIO.so > 0x2300000 - 0x232ffff libTix8.4.dylib /Applications/Chimera.app/ >Contents/Resources/lib/Tix8.4/libTix8.4.dylib > 0x250d000 - 0x2529fff GLDriver /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Resources/GLDriver.bundle/GLDriver > 0x2530000 - 0x2554fff GLRendererFloat /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat > 0x255b000 - 0x2561fff libTogl2.0.dylib /Applications/Chimera.app/ >Contents/Resources/lib/Togl2.0/libTogl2.0.dylib > 0x2568000 - 0x2576fff libXmu.6.dylib /usr/X11R6/lib/libXmu.6.dylib > 0x257e000 - 0x25b7fff libXt.6.dylib /usr/X11R6/lib/libXt.6.dylib > 0x25cb000 - 0x25cffff libSM.6.dylib /usr/X11R6/lib/libSM.6.dylib > 0x25d4000 - 0x25e3fff libICE.6.dylib /usr/X11R6/lib/libICE.6.dylib > 0x2705000 - 0x285efff GLEngine /System/Library/Frameworks/ >OpenGL.framework/Resources/GLEngine.bundle/GLEngine > 0x288a000 - 0x29fafff com.apple.GeForceFXGLDriver 1.4.40 (4.4.0) > /System/Library/Extensions/GeForceFXGLDriver.bundle/Contents/MacOS/ >GeForceFXGLDriver > 0x2b9b000 - 0x2b9cfff _collaboratory.so > /Applications/Chimera.app/Contents/Resources/lib/_collaboratory.so > 0x2c99000 - 0x2c9cfff _AE.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_AE.so > 0x2caf000 - 0x2cb0fff _Evt.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_Evt.so > 0x2cbe000 - 0x2cc0fff struct.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/struct.so > 0x2cd8000 - 0x2cdefff _File.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_File.so > 0x2e1f000 - 0x2e22fff _Res.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_Res.so > 0x33b2000 - 0x33b3fff collections.so /Applications/Chimera.app/ >Contents/Resources/lib/python2.4/lib-dynload/collections.so > 0x3505000 - 0x3509fff multiarray.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/Numeric/multiarray.so > 0x3519000 - 0x3529fff _numpy.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/Numeric/_numpy.so > 0x355e000 - 0x356afff umath.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/Numeric/umath.so > 0x35d9000 - 0x3688fff lapack_lite.so /Applications/Chimera.app/ >Contents/Resources/lib/python2.4/site-packages/Numeric/lapack_lite.so > 0x3791000 - 0x3797fff ranlib.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/Numeric/ranlib.so > 0x37ee000 - 0x380efff _volume.so /Applications/Chimera.app/Contents/ >Resources/lib/_volume.so > 0x386e000 - 0x3891fff _surface.so /Applications/Chimera.app/Contents/ >Resources/lib/_surface.so > 0x3961000 - 0x3974fff _contour.so /Applications/Chimera.app/Contents/ >Resources/lib/_contour.so > 0xa000000 - 0xa081fff libtcl8.4.dylib /Applications/Chimera.app/ >Contents/Resources/lib/libtcl8.4.dylib > 0xb000000 - 0xb0a9fff libtk8.4.dylib /Applications/Chimera.app/ >Contents/Resources/lib/libtk8.4.dylib >0x8fe00000 - 0x8fe49fff dyld 46.9 /usr/lib/dyld >0x90000000 - 0x9016ffff libSystem.B.dylib > /usr/lib/libSystem.B.dylib >0x901bf000 - 0x901c1fff libmathCommon.A.dylib > /usr/lib/system/libmathCommon.A.dylib >0x901c3000 - 0x90200fff com.apple.CoreText 1.1.1 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/CoreText.framework/Versions/A/CoreText >0x90227000 - 0x902fcfff ATS /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/ >A/ATS >0x9031c000 - 0x90770fff com.apple.CoreGraphics 1.258.38 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics >0x90807000 - 0x908cffff com.apple.CoreFoundation 6.4.6 (368.27) > /System/Library/Frameworks/CoreFoundation.framework/Versions/A/ >CoreFoundation >0x9090d000 - 0x9090dfff com.apple.CoreServices 10.4 (???) > /System/Library/Frameworks/CoreServices.framework/Versions/A/ >CoreServices >0x9090f000 - 0x90a02fff libicucore.A.dylib > /usr/lib/libicucore.A.dylib >0x90a52000 - 0x90ad1fff libobjc.A.dylib /usr/lib/libobjc.A.dylib >0x90afa000 - 0x90b5efff libstdc++.6.dylib > /usr/lib/libstdc++.6.dylib >0x90bcd000 - 0x90bd4fff libgcc_s.1.dylib /usr/lib/libgcc_s.1.dylib >0x90bd9000 - 0x90c4cfff com.apple.framework.IOKit 1.4.6 (???) > /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit >0x90c61000 - 0x90c73fff libauto.dylib /usr/lib/libauto.dylib >0x90c79000 - 0x90f1ffff com.apple.CoreServices.CarbonCore 682.15 > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >CarbonCore.framework/Versions/A/CarbonCore >0x90f62000 - 0x90fcafff com.apple.CoreServices.OSServices 4.1 > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >OSServices.framework/Versions/A/OSServices >0x91003000 - 0x91041fff com.apple.CFNetwork 129.18 > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >CFNetwork.framework/Versions/A/CFNetwork >0x91054000 - 0x91064fff com.apple.WebServices 1.1.3 (1.1.0) > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >WebServicesCore.framework/Versions/A/WebServicesCore >0x9106f000 - 0x910eefff com.apple.SearchKit 1.0.5 > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >SearchKit.framework/Versions/A/SearchKit >0x91128000 - 0x91146fff com.apple.Metadata 10.4.4 (121.36) > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >Metadata.framework/Versions/A/Metadata >0x91152000 - 0x91160fff libz.1.dylib /usr/lib/libz.1.dylib >0x91163000 - 0x91302fff com.apple.security 4.5.1 (29002) > /System/Library/Frameworks/Security.framework/Versions/A/Security >0x91400000 - 0x91408fff com.apple.DiskArbitration 2.1.1 > /System/Library/Frameworks/DiskArbitration.framework/Versions/A/ >DiskArbitration >0x9140f000 - 0x91435fff com.apple.SystemConfiguration 1.8.6 > /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/ >SystemConfiguration >0x91447000 - 0x9144efff libbsm.dylib /usr/lib/libbsm.dylib >0x91452000 - 0x914c8fff com.apple.audio.CoreAudio 3.0.4 > /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio >0x91519000 - 0x91519fff com.apple.ApplicationServices 10.4 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >ApplicationServices >0x9151b000 - 0x91547fff com.apple.AE 314 (313) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/AE.framework/Versions/A/AE >0x9155a000 - 0x9162efff com.apple.ColorSync 4.4.8 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/ColorSync.framework/Versions/A/ColorSync >0x91669000 - 0x916dcfff com.apple.print.framework.PrintCore 4.6 (177.13) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/PrintCore.framework/Versions/A/PrintCore >0x9170a000 - 0x917b3fff com.apple.QD 3.10.21 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/QD.framework/Versions/A/QD >0x917d9000 - 0x91824fff com.apple.HIServices 1.5.2 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/HIServices.framework/Versions/A/HIServices >0x91843000 - 0x91859fff com.apple.LangAnalysis 1.6.3 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis >0x91865000 - 0x91880fff com.apple.FindByContent 1.5 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/FindByContent.framework/Versions/A/FindByContent >0x9188b000 - 0x918c8fff com.apple.LaunchServices 181 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/LaunchServices.framework/Versions/A/LaunchServices >0x918dc000 - 0x918e8fff com.apple.speech.synthesis.framework 3.5 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis >0x918ef000 - 0x9192afff com.apple.ImageIO.framework 1.5.0 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/ImageIO.framework/Versions/A/ImageIO >0x9193c000 - 0x919eefff libcrypto.0.9.7.dylib > /usr/lib/libcrypto.0.9.7.dylib >0x91a34000 - 0x91a4afff libcups.2.dylib /usr/lib/libcups.2.dylib >0x91a4f000 - 0x91a6dfff libJPEG.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libJPEG.dylib >0x91a72000 - 0x91ad0fff libJP2.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libJP2.dylib >0x91ae2000 - 0x91ae6fff libGIF.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libGIF.dylib >0x91ae8000 - 0x91b65fff libRaw.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libRaw.dylib >0x91b69000 - 0x91ba6fff libTIFF.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libTIFF.dylib >0x91bac000 - 0x91bc6fff libPng.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libPng.dylib >0x91bcb000 - 0x91bcdfff libRadiance.dylib > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib >0x91bcf000 - 0x91bcffff com.apple.Accelerate 1.3.1 (Accelerate 1.3.1) > /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate >0x91bd1000 - 0x91c5ffff com.apple.vImage 2.5 > /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ >vImage.framework/Versions/A/vImage >0x91c66000 - 0x91c66fff com.apple.Accelerate.vecLib 3.3.1 (vecLib 3.3.1) > /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ >vecLib.framework/Versions/A/vecLib >0x91c68000 - 0x91cc1fff libvMisc.dylib /System/Library/Frameworks/ >Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/ >libvMisc.dylib >0x91cca000 - 0x91ceefff libvDSP.dylib /System/Library/Frameworks/ >Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/ >libvDSP.dylib >0x91cf6000 - 0x920fffff libBLAS.dylib /System/Library/Frameworks/ >Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/ >libBLAS.dylib >0x92139000 - 0x924edfff libLAPACK.dylib /System/Library/Frameworks/ >Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/ >libLAPACK.dylib >0x9251a000 - 0x92597fff com.apple.DesktopServices 1.3.4 > /System/Library/PrivateFrameworks/DesktopServicesPriv.framework/ >Versions/A/DesktopServicesPriv >0x925d8000 - 0x92808fff com.apple.Foundation 6.4.7 (567.28) > /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation >0x92914000 - 0x929f2fff libxml2.2.dylib /usr/lib/libxml2.2.dylib >0x92a0f000 - 0x92afcfff libiconv.2.dylib /usr/lib/libiconv.2.dylib >0x92b0c000 - 0x92b23fff libGL.dylib /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Libraries/libGL.dylib >0x92b2e000 - 0x92b86fff libGLU.dylib /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Libraries/libGLU.dylib >0x92b9a000 - 0x92b9afff com.apple.Carbon 10.4 (???) > /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon >0x92b9c000 - 0x92bacfff com.apple.ImageCapture 3.0.4 > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >ImageCapture.framework/Versions/A/ImageCapture >0x92bbb000 - 0x92bc3fff com.apple.speech.recognition.framework 3.6 > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >SpeechRecognition.framework/Versions/A/SpeechRecognition >0x92bc9000 - 0x92bcffff com.apple.securityhi 2.0.1 (24742) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >SecurityHI.framework/Versions/A/SecurityHI >0x92bd5000 - 0x92c66fff com.apple.ink.framework 101.2.1 (71) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >Ink.framework/Versions/A/Ink >0x92c7a000 - 0x92c7efff com.apple.help 1.0.3 (32.1) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >Help.framework/Versions/A/Help >0x92c81000 - 0x92c9ffff com.apple.openscripting 1.2.5 (???) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >OpenScripting.framework/Versions/A/OpenScripting >0x92cb1000 - 0x92cb7fff com.apple.print.framework.Print 5.2 (192.4) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >Print.framework/Versions/A/Print >0x92cbd000 - 0x92d20fff com.apple.htmlrendering 66.1 (1.1.3) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >HTMLRendering.framework/Versions/A/HTMLRendering >0x92d47000 - 0x92d88fff com.apple.NavigationServices 3.4.4 (3.4.3) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >NavigationServices.framework/Versions/A/NavigationServices >0x92daf000 - 0x92dbdfff com.apple.audio.SoundManager 3.9.1 > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >CarbonSound.framework/Versions/A/CarbonSound >0x92dc4000 - 0x92dc9fff com.apple.CommonPanels 1.2.3 (73) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >CommonPanels.framework/Versions/A/CommonPanels >0x92dce000 - 0x930c2fff com.apple.HIToolbox 1.4.8 (???) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >HIToolbox.framework/Versions/A/HIToolbox >0x931c8000 - 0x931d3fff com.apple.opengl 1.4.12 > /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL >0x94096000 - 0x940d0fff libGLImage.dylib /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Libraries/libGLImage.dylib >0x9492b000 - 0x94950fff libssl.0.9.7.dylib > /usr/lib/libssl.0.9.7.dylib >0x96451000 - 0x96451fff com.apple.vecLib 3.3.1 (vecLib 3.3.1) > /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib >0x969cb000 - 0x96a99fff libGLProgrammability.dylib > /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/ >libGLProgrammability.dylib >0x96ab4000 - 0x96ab5fff libGLSystem.dylib > /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/ >libGLSystem.dylib >0x99756000 - 0x99762fff libXplugin.1.dylib > /usr/lib/libXplugin.1.dylib > >Model: MacPro1,1, BootROM MP11.005C.B01, 4 processors, Dual-Core Intel Xeon, >2.66 GHz, 5 GB >Graphics: NVIDIA Quadro FX 4500, NVIDIA Quadro FX 4500, PCIe, 512 MB >Memory Module: DIMM Riser A/DIMM 1, 512 MB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser A/DIMM 2, 512 MB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser B/DIMM 1, 1 GB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser B/DIMM 2, 1 GB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser A/DIMM 3, 1 GB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser A/DIMM 4, 1 GB, DDR2 FB-DIMM, 667 MHz >Network Service: Built-in Ethernet 1, Ethernet, en0 >PCI Card: NVIDIA Quadro FX 4500, Display, Slot-1 >Serial ATA Device: ST3250824AS P, 232.89 GB >Parallel ATA Device: SONY DVD RW DW-D150A >USB Device: Hub in Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec, >500 mA >USB Device: Apple Optical USB Mouse, Primax Electronics, Up to 1.5 Mb/sec, >100 mA >USB Device: Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec, 250 mA >FireWire Device: built-in_hub, unknown_value, Unknown > > >___________________________________________________________ >Peter Engelhardt, PhD, docent >Assistant Professor in Molecular Genetics >Unit of Molecular Electron Tomography >Department of Pathology and Virology >Haartman Institute >P.O.Box 21, FIN-00014 Univ. of Helsinki, Finland >Visiting Address: Haartmaninkatu 3, Helsinki >Office Tel: (+358-9)-19126431 (direct) >Laboratory Tel: (+358-9)-19126441 >EM-facilities, Tel: (+358-9)-19126885 >Digiroom: Tel: (+358-9)-1912886 >Fax: (+358-9)-19126491 >FIN-00014 Univ. of Helsinki, Helsinki, Finland > >LCE, Laboratory of Computational Engineering, >Research Center for Computational Science and Engineering >Helsinki University of Technology (HUT), >P.O.Box 9203, FIN-02015 HUT, FINLAND >Visiting Address: Innopolis2, Tekniikantie 14, Espoo > >Home address: > Lindstedstvägen 1 B 7 > FIN-02700 Grankulla, > Finland >Tel: (+358-9)-5091381 > > Mobil Phone: +358 (0)415610171 > Email: Peter.Engelhardt(a)Helsinki.Fi > URL: http://www.lce.hut.fi/~engelhar/ -- ___________________________________________________________ Peter Engelhardt, PhD, docent Assistant Professor in Molecular Genetics Unit of Molecular Electron Tomography Department of Pathology and Virology Haartman Institute P.O.Box 21, FI-00014 Univ. of Helsinki, Finland Visiting Address: Haartmaninkatu 3, Helsinki Office Tel: (+358-9)-19126431 (direct) Laboratory Tel: (+358-9)-19126729, 19126442 EM-facilities, Tel: (+358-9)-19126885 Fax: (+358-9)-19126700 Laboratory of Computational Engineering, Research Center for Computational Science and Engineering Helsinki University of Technology (HUT), P.O.Box 9203, FI-02015 HUT, FINLAND Visiting Address: Innopolis2, Tekniikantie 14, Espoo Office Tel: (+358-9)-4514843 (direct) Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: (+358-9)-5091381 Mobile Phone: +358-(0)41 561 0171 Email: Peter.Engelhardt(a)Helsinki.Fi URL: http://www.lce.hut.fi/~engelhar/

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queries on making image
by bala 09 Nov '06

09 Nov '06

Hello chimera users, 1) I hve to show two molecules in the same figure side by side. When i am displaying, i have a problem that both molecules are not coming at same plane. Is there any option to adjust this. 2) I labelled both these molecules. The labels are coming fine in the screen. But when i create an image (i save it as tif file), some labels are getting hided below my molecular surface. Which option i should use to rectify that. 3) How one can add text on the screen/near a particular spot on the molecule ? 4) Someone kindly Suggest me on best settings (i mean values) of the resolution based on your experience of making figures using chimera or which you normally use. Thanks in advance, Bala

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Re: [Chimera-users] font change in v1.2303+
by Sabuj Pattanayek 07 Nov '06

07 Nov '06

Hi, Yes, now that you mention it I think we have confused each other. I am talking about the fonts in the widgets and dialogs and not the annotation fonts in the linux version. I will grab an old install from http://www.cgl.ucsf.edu/chimera/olddownload.html, and make a screenshot comparing that with the latest 1.2304. I don't think I saw this change in the WinXP version, but I'll check that too. Thanks, Sabuj Elaine Meng wrote: > Hi Sabuj, > It seems like Greg's response was about the labels on the structures, > whereas you said "gui" which I interpret as the widgets and dialogs. > Were you asking about these? I noticed that the font for the "Really > Exit?" dialog is now different, but I haven't seen differences in other > dialogs. > Elaine

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sparky-chimera error
by ksgodin＠u.washington.edu 07 Nov '06

07 Nov '06

Hi all, I having been trying to open an ensemble of NMR structures with the 'km' feature of Sparky. Everything opens fine, but the Model Panel does not open properly. The error log sites Program Files\Sparky\python\lib-tk\Tix.py, line 477, in_init_ self.stylename=self.tk.call ('tixDisplayStyle', itemtype, TclError: invalid command name "tixDisplayStyle" Does anyone know how to fix this? It comes up with Sparky 3.111 and Chimera 1.2065 or 1.1195. Thanks, Kate ~~~~~~~~~~~~~~~~~~~~~~ Kate Godin UW Chemistry Dept Varani Group BAG 63 ~~~~~~~~~~~~~~~~~~~~~~

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font change in v1.2303+
by Sabuj Pattanayek 04 Nov '06

04 Nov '06

Hi, The gui font seems to have changed in v1.2303+ . Is there some way to change it back to the old font? Thanks, Sabuj

2 2

stereo
by hsosa＠aecom.yu.edu 03 Nov '06

03 Nov '06

How can I use stereo (sequential mode) ?. If I click the stereo button in the camera dialog or start chimera using the command chimera --stereo. I get the error message: Unable to turn on stereo viewing Unable to find hardware stereo support (coulddm't choose stereo pixel format Couldn't figure togl widget) My graphic cards is a NVIDIA Quadro4 900 XGL. The Nvdia Stereo driver (v: 91.31) is installed and enabled. Chimera version is: 1 build 2255 2006/06/23 Monitors: Two (dual) digital DELL 1900 FP Computer: Dual Xeon 1.4 Ghz, 1GB of RAM. Running Windows XP Thanks Hernando --

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Showing data set axes
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, Chimera supports a format for making geometric objects called BILD described in the Chimera manual: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Below is a 6 line BILD file that when opened in Chimera shows cylindrical arrows for the X (red), (green), and Z (blue) axes in the style of the program VMD. I made the axes 20 units long, with radius 1 and cone shaped tip with a radius of 2. Tom ----- File axes.bld: .color 1 0 0 .arrow 0 0 0 20 0 0 1 2 .color 0 1 0 .arrow 0 0 0 0 20 0 1 2 .color 0 0 1 .arrow 0 0 0 0 0 20 1 2 > From: Jeff > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Subject: RE: Chimera length units > Date: Thu, 2 Nov 2006 17:30:29 -0800 > > i figured some of that but is good to hear it from the source. > > one last question - if i want to make an origin with axes (like a CAD > program might have) so i don't get lost after rotating my volumes a jillion > times and have to click 'orient', is there a way for me to make a > marker-based model (two markers for each axis) and put it slightly > off-origin (like in the -,-,- octant) so that i have a visual on my axes as > i rotate the scene? > > as in, is there a simple way for me to hand-write a marker model that i can > just load and fix to the scene? > > thanks, > > -jeff

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