April 2005 - Chimera-dev - RBVI Mailing Lists

add h
by Virginie Lafont 01 May '09

01 May '09

Hi, I am a new user of chimera and I already have a question. I have an protonated aspartic acid in my protein and I was wondering, is it possible to add hydrogen atom to aspartic acid with chimera? Thanks Virginie

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installation problem in linux
by venkataraman kabaleeswaran 02 May '05

02 May '05

hi i had a following problem while install the chimera on linux, ./chimera OpenGL misconfiguration detected. /usr/lib/libGL.so.1 differs from /usr/X11R6/lib/libGL.so.1. Please read installation instructions. any help thanks vk Kabaleeswaran Venkataraman Arise, Awake and stop not until goal is Reached - Swami Vivekanand __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Program code
by Jesse Parker 26 Apr '05

26 Apr '05

To Whom it May Concern, I am currently looking for ways of visualizing proteins as they are being folded by a matlab program we are developing here at the University of Connecticut. I am unsure whether an extension would be adequate to read and write to matlab, or modifications to the chimera source would be necesarry. Would it be possible to get a copy of the source code for Chimera and possibly some examples of extensions? Thanks for your time, Jesse Parker ME Graduate Student University of Connecticut

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RE: [chimera-dev] accelerators and stereo]
by Greg Couch 19 Apr '05

19 Apr '05

Hi Matt, I'm responsible for chimera's stereo support. Can you send me the output of /usr/gfx/gfxinfo so I can figure what which graphics option you have. And I'd also like to know if chimera is switching the display into stereo mode or if you do it by hand (for instance, because you're displaying remotely on to your SGI). Chances are that if you have a semi-recent SGI workstation you can use an alternate stereo mode that doesn't loose as much resolution. And also please send me the output from "CHIMERA/bin/autostereod -f -v" -- autostereod is a daemon that chimera uses to switch the monitor into stereo mode on SGIs, -f says to run in the foreground, and -v says to be verbose. You can ^C the program after it outputs which stereo mode it would switch the monitor to. There's a chance that the autostereod program is not picking the right stereo monitor (setmon) mode. Your explanation about the stereo quarter of the screen is confusing to me because the whole monitor screen is in stereo. Perhaps you're talking about a screen in the X11 sense and you have your X11 screen set to 1600x1200 and when you switch into stereo, you're getting interlaced stereo with 1280x512 resolution? I'm not sure how else you would get a stereo quarter. Normally, SGI monitors are configured to be 1280x1024 non-interlaced and older SGIs use an 1280x492 interlaced mode (492 instead of 512 to account for the vertical retrace of the monitor between stereo frames). So in interlaced stereo you only loose half of the vertical resolution, and not any of the horizontal resolution. If you're using the SGI defaults, the mouse should always be visible on the display, but you may have to move it between the left and right eye view by rolling off the bottom (to the top of the other eye) or vice-versa. Greg Couch UCSF Computer Graphics Lab gregc(a)cgl.ucsf.edu On Tue, 19 Apr 2005, Thomas Goddard wrote: > Date: Tue, 19 Apr 2005 14:19:03 -0700 (PDT) > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > To: gregc(a)cgl.ucsf.edu > Subject: [matthewd(a)bcm.tmc.edu: RE: [chimera-dev] accelerators and stereo] > > Hi Greg, > > Do you have any suggestion about this chimera-dev post about ancient > SGI stereo resulting in Chimera windows being placed off the viewable > screen? > > Tom > > ------- Start of forwarded message ------- > Matthew Dougherty matthewd at bcm.tmc.edu > Tue Apr 19 14:16:07 PDT 2005 > > another thing about stereo. > > it would good to have all the dialogs come up in the stereo quarter of the > display when I am in stereo mode. it appears the dialogs come up randomly on > the display. sometimes the main chimera window comes up > not-on-the-stereo-section of the display so you can't force it into > monographics. > > > matthew > > ------------------------------------------ > Matthew Dougherty/713-433-3849 > National Center for Macromolecular Imaging > Baylor College of Medicine > > > Date: Tue, 19 Apr 2005 15:08:05 -0500 > From: Matthew Dougherty <matthewd(a)bcm.tmc.edu> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Cc: chimera-dev <chimera-dev(a)cgl.ucsf.edu> > Subject: RE: [chimera-dev] accelerators and stereo > >> ===== Original Message From Thomas Goddard <goddard(a)cgl.ucsf.edu> ===== >> Hi Matthew, >> >> I don't understand what you mean by "the stereo quarter of the display". >> Is this some special monitor? >> > > standard monitor & graphics hardware. > when stereo hardware is engaged (ircombine or setmon), the computer reduces > the display by two on each axis. It does this to create the left and right > display > buffers out of the single monographic display buffer, a limited graphical > resource. > > when it sends out the stereo display buffers it doubles the output pixels, > hence the objects (e.g. desktop icons) look twice as big. What used to take > one pixel to display is now using four pixels. > > at the same time the emitter activates the googles, polarizing (making opaque) > one eye, and transparent the other; on the screen the two display buffers, > are put on the display, alternating typically 1/30 apart. > > > most people use the top left area/ top quarter, where the tool chest is > located, typical default for sgi, but can be overridden. > > unfortunately, when stereo mode is engaged the screen size is not adjusted > within the x window manager as it should be (SGI or X design bug), so you have > anomalies like the mouse being able to go off the visible display, or allowing > windows to startup off the visible display; because the x window manager is > working with 1024x1200 (mono) when in reality the display area is 512x600 > (stereo). This may be solvable by application code. > > >> Chimera uses stereo in a window provided by the OpenGL graphics library. >> > which gets it from the x window manager > >> Chimera does not provide a way to specify the starting positions of >> its windows. Initial placement of windows is usually managed by your >> windowing system, not by individual applications. >> >> Tom > > - ------------------------------------------ > Matthew Dougherty/713-433-3849 > National Center for Macromolecular Imaging > Baylor College of Medicine > ------- End of forwarded message ------- >

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Re: [chimera-dev] accelerators and stereo
by Thomas Goddard 19 Apr '05

19 Apr '05

Hi Matthew, Ok I think I have it right now. The code below where I've added a second argument to the c.setMode() call now makes the F1 function key toggle between stereo and mono. Sorry the previous code did not work. I tested it with "cross-eye stereo" because my machine did not have hardware stereo and that worked with the previous code. But when I tested with hardware stereo I found that it needed the second argument to the setMode() function. Tom --- ChimeraExtension.py code follows # ----------------------------------------------------------------------------- # import chimera.extension # ----------------------------------------------------------------------------- # class Stereo_Mono_EMO(chimera.extension.EMO): def name(self): return 'Stereo / Mono' def description(self): return 'Toggle between stereo and mono modes' def categories(self): return ['Utilities'] def icon(self): return None def activate(self): import chimera c = chimera.viewer.camera if c.mode() == 'stereo': c.setMode('mono', chimera.viewer) else: if not c.setMode('stereo', chimera.viewer): from chimera import replyobj replyobj.status('Start chimera with the --stereo command-line switch to enable stereo') # # Chimera camera modes: # 'VRex row stereo', 'cross-eye stereo', 'mono', 'stereo', # 'stereo left eye', 'stereo right eye', 'wall-eye stereo' # # ----------------------------------------------------------------------------- # emo = Stereo_Mono_EMO(__file__) chimera.extension.manager.registerExtension(emo) from chimera.tkgui import app app.bind('<KeyPress-F1>', lambda event, emo=emo: emo.activate()) app.graphics.bind('<KeyPress-F1>', lambda event, emo=emo: emo.activate())

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RE: [chimera-dev] accelerators and stereo
by Matthew Dougherty 19 Apr '05

19 Apr '05

>===== Original Message From Thomas Goddard <goddard(a)cgl.ucsf.edu> ===== >Hi Matthew, > > I don't understand what you mean by "the stereo quarter of the display". >Is this some special monitor? > standard monitor & graphics hardware. when stereo hardware is engaged (ircombine or setmon), the computer reduces the display by two on each axis. It does this to create the left and right display buffers out of the single monographic display buffer, a limited graphical resource. when it sends out the stereo display buffers it doubles the output pixels, hence the objects (e.g. desktop icons) look twice as big. What used to take one pixel to display is now using four pixels. at the same time the emitter activates the googles, polarizing (making opaque) one eye, and transparent the other; on the screen the two display buffers, are put on the display, alternating typically 1/30 apart. most people use the top left area/ top quarter, where the tool chest is located, typical default for sgi, but can be overridden. unfortunately, when stereo mode is engaged the screen size is not adjusted within the x window manager as it should be (SGI or X design bug), so you have anomalies like the mouse being able to go off the visible display, or allowing windows to startup off the visible display; because the x window manager is working with 1024x1200 (mono) when in reality the display area is 512x600 (stereo). This may be solvable by application code. > Chimera uses stereo in a window provided by the OpenGL graphics library. > which gets it from the x window manager > Chimera does not provide a way to specify the starting positions of >its windows. Initial placement of windows is usually managed by your >windowing system, not by individual applications. > > Tom ------------------------------------------ Matthew Dougherty/713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine

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RE: [chimera-dev] accelerators and stereo
by Matthew Dougherty 19 Apr '05

19 Apr '05

another thing about stereo. it would good to have all the dialogs come up in the stereo quarter of the display when I am in stereo mode. it appears the dialogs come up randomly on the display. sometimes the main chimera window comes up not-on-the-stereo-section of the display so you can't force it into monographics. matthew ------------------------------------------ Matthew Dougherty/713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine

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RE: [chimera-dev] accelerators and stereo
by Matthew Dougherty 19 Apr '05

19 Apr '05

Hi Eric and Tom thanks for the code accelerator example. definetly want to have it use the f1 button matt >===== Original Message From Eric Pettersen <pett(a)cgl.ucsf.edu> ===== >It is also possibly to have the F1 button do the toggling, if that is >specifically what you require. If it is, let me know and I can provide >details. > >--Eric > >On Apr 19, 2005, at 10:10 AM, Thomas Goddard wrote: > >> Hi Matthew, >> >> Below is some Python code to make a button to toggle between stereo >> and mono viewing in Chimera. I assumed you mean hardware stereo (LCD >> or polarized glasses, or special monitor). You can adapt the code to >> toggle to cross-eye or wall-eye stereo by changing 'stereo' to >> 'cross-eye stereo' or 'wall-eye stereo' in the code. >> >> Make a directory in you Chimera distribution chimera/share/Stereo >> (directory name does not matter) and put the code below in a file >> ChimeraExtension.py (name does matter). This will add a >> Tools->Utilities->Stereo/Mono menu entry to toggle modes. >> >> To put a button for this on the Chimera main window use >> Favorites/Preferences under Category tools you'll see all the Tools >> menu entries listed in order. Find Utilities->Stereo/Mono and turn on >> the checkbutton in the "On Toolbar" (second) column. The button will >> show up on the left edge of the main Chimera window. Press the Save >> button at the bottom of the Preferences dialog if you want this button >> to be on the main window every time you start Chimera. >> >> Tom >> >> >> >> ------ >> ChimeraExtension.py code follows: >> >> # >> ----------------------------------------------------------------------- >> ------ >> # >> import chimera.extension >> >> # >> ----------------------------------------------------------------------- >> ------ >> # >> class Stereo_Mono_EMO(chimera.extension.EMO): >> >> def name(self): >> return 'Stereo / Mono' >> def description(self): >> return 'Toggle between stereo and mono modes' >> def categories(self): >> return ['Utilities'] >> def icon(self): >> return None >> def activate(self): >> import chimera >> c = chimera.viewer.camera >> if c.mode() == 'stereo': >> c.setMode('mono') >> else: >> if not c.setMode('stereo'): >> from chimera import replyobj >> replyobj.status('Start chimera with the --stereo command-line switch >> to enable stereo') >> # >> # Chimera camera modes: >> # 'VRex row stereo', 'cross-eye stereo', 'mono', 'stereo', >> # 'stereo left eye', 'stereo right eye', 'wall-eye stereo' >> # >> >> # >> ----------------------------------------------------------------------- >> ------ >> # >> chimera.extension.manager.registerExtension(Stereo_Mono_EMO(__file__)) >> >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev ------------------------------------------ Matthew Dougherty/713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine

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accelerators and stereo
by Matthew Dougherty 19 Apr '05

19 Apr '05

I would like to have the f1 key do stereo/mono. can you recommend a change I can make? ------------------------------------------ Matthew Dougherty/713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine

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[chimera-dev] residue.atoms, atom.bonds, coords, static class methods
by Eric Pettersen 18 Apr '05

18 Apr '05

This is a heads up that the next release of Chimera (ETA some time this summer) will have had a major reworking of the internals, which will have some visible effects in the Python layer. There will be four important Python-layer changes: 1) The Residue class method atoms() will return a list of Atoms. Currently atoms() returns a dictionary keyed with atom names that yields a list of Atoms with the corresponding name. This makes it awkward to simply iterate through the atoms of a residue, although the somewhat-obscure method oslChildren() of Residue does currently return a list of Atoms (and will continue to do so). A list of the atom names will be available as atomNames(). The name->atom-list dictionary will remain available, but will be named atomsMap(). 2) The Atom class method bonds() will return a list of Bonds. Currently bonds() is a dictionary whose keys are the Atoms bound to this atom, and whose values are the Bonds connecting them. Instead, the bonds() method will return a list of the Bonds, and the neighbors() method will return a list of the bonded Atoms (in the same order). The old bonds() functionality will remain available as the bondsMap() method. 3) Coord goes away The coord() and xformCoord() methods will return Points instead of Coords. Relevant methods of Coord (e.g. dist(), sqDist()) will be added to Point. 4) Class method renaming Class methods names were indicated by a leading class name and underscore (e.g. Xform_identity()). Now they are indicated with the class name followed by a dot (e.g. Xform.identity()). Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Chimera-dev April 2005