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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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many duplicated libraries
by David E. Konerding 11 Apr '05

11 Apr '05

I just noticed: in the lib/ dir of chimera, many of the shared libraries is duplicated multiple times: dek@bosshog:~/outsrc/Mesa-6.2.1 :ls -il ~/sw/chimera/chimera-1.2065/lib/libGL* 1939030 -rwxrwxr-x 1 dek griddev 551543 Dec 16 12:54 /home/portnoy/u5/dek/sw/chimera/chimera-1.2065/lib/libGLU.so 1939031 -rwxrwxr-x 1 dek griddev 551543 Dec 16 12:54 /home/portnoy/u5/dek/sw/chimera/chimera-1.2065/lib/libGLU.so.1 1939021 -rwxrwxr-x 1 dek griddev 551543 Dec 16 12:54 /home/portnoy/u5/dek/sw/chimera/chimera-1.2065/lib/libGLU.so.1.3.060001 where these should be links. Yeah, I know that zip doesn't realy support links but do you guys really want to be shipping all three copies? Dave

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C++ headers
by Eric Pettersen 28 Mar '05

28 Mar '05

Hi, We've made Chimera's C++ header files available for download from the Programmer's Guide main page: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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[chimera-dev] Re: [Chimera-users] Zones to create inspector list of "contacts"
by Eric Pettersen 24 Mar '05

24 Mar '05

Tom, Wanted to alert you to a couple of functions in chimera.misc that will be in the next _production_ release: getAtoms(atomContainer) returns a list of atoms from various things (or lists of things) that can contain atoms, such as residues, sequences, molecules atomSearchTree(atomContainer, sepVal=5.0) returns a adaptive search tree of the atoms in the atomContainer (ala arg to getAtoms()). CGLutil.AdaptiveTree has docs for these trees. Typically searched with the 'searchTree' method. --Eric On Mar 23, 2005, at 11:37 AM, Thomas Goddard wrote: > Hi Grant, > > Below is some Python code that will create pseudobonds between all > pairs of selected atoms from different molecules that are within 3 > angstroms. > It is quite slow for large sets of selected atoms. It could be made > much > faster but I chose to keep it simple. > > Tom > > # > ----------------------------------------------------------------------- > ----- > # Check all pairwise distances between selected atoms and connect those > # atom pairs that are close by a pseudobond if the atoms belong to > different > # molecules. > # > # To run this use Tools / Programming / Idle to show the Python shell > and > # type > # > # >>> execfile('path-to-this-file.py') > # > # For large selected sets of atoms this will be slow. > # > > # > ----------------------------------------------------------------------- > ----- > # > def connect_close(dist): > > from chimera import selection, distance > atoms = selection.currentAtoms() > atom_pairs = [] > n = len(atoms) > for i1 in range(n): > a1 = atoms[i1] > for i2 in range(i1+1, n): > a2 = atoms[i2] > if a1.molecule != a2.molecule: > if distance(a1.xformCoord().xyz, a2.xformCoord().xyz) > <= dist: > atom_pairs.append((a1,a2)) > print len(atom_pairs), 'atom pairs' > > from chimera import PseudoBondGroup, PseudoBondMgr_mgr, PseudoBond > pg = PseudoBondMgr_mgr().newPseudoBondGroup('close contacts') > bonds = [] > for a1, a2 in atom_pairs: > bonds.append(pg.newPseudoBond(a1, a2)) > > import chimera > chimera.openModels.add([pg]) > > selection.setCurrent(bonds) > > # > ----------------------------------------------------------------------- > ----- > # > connect_close(3) > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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mrc file format difference in win-linux ??
by shrikant gutta 17 Mar '05

17 Mar '05

Hi all, I was working on the mrc file format difference between that of windows and linux. I couldnt figure out the difference between these file formats. (My job is to modify prog code to read linux_mrc`s on a windows software which can already read win_mrc`s in C++) I had got one site saying abt MRC specs: http://ami.scripps.edu/prtl_data/mrc_specification.htm i guess this site says abt win_mrc format no abt lin_mrc`s. I couldnt find anymore clues for my problem. Thanks & Regards Gutta __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Extensions with C code
by Thomas Goddard 01 Nov '04

01 Nov '04

Jerome Nilmeier has some questions about writing C code extensions to Chimera. ------- Start of forwarded message ------- Date: Sun, 31 Oct 2004 18:42:34 -0800 (PST) From: Jerome Nilmeier <jnilmeier(a)yahoo.com> Subject: rudimentary chimera questions To: goddard(a)cgl.ucsf.edu Hello Tom: I'm not sure exactly who to ask about this... I am a UCSF grad student, and I'd like to use chimera for my reserach. I am thinking of trying to interface some c code with chimera, and had just a couple of basic questions: 1) how do you access the information about loaded molecules from the idle prompt? I went through the example, but it doesn't say how to work with molecules that have been loaded using the menu. 2) I was trying to use swig to generate a python wrapper...so far without success. Do you have a recommended (hopefully straightforward) method for interfacing python with c code? Any help you could offer would be most appreciated. Thank you, Jerome ------- End of forwarded message -------

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