- Chimera-dev - RBVI Mailing Lists

Recent API changes
by Greg Couch 18 Oct '05

18 Oct '05

Hello Developers, In the recent chimera release candidates and the imminent 1.2180 production release, there several API changes that may trip up existing code. Many of these changes are due to our improved method of moving data between Python and the underlying C++ layer (roughly 2X faster). Most of the changes are detailed below. Greg Couch gregc(a)cgl.ucsf.edu ------ The new code works much better with the Python help function. In the IDLE window, try help(chimera.Atom) and you'll see all of Atom's methods and their argument types and return values. For the changes below assume: m is a Molecule r is a Residue a is an Atom b is a Bond x is a Xform Atoms have a simpified interface to their bonds: a.bonds() returns a list of bonds a.neighbors() returns a list of adjacent atoms (via bonds) a.bondsMap() is both of the above combined as a dictionary and is what a.bonds() used to return If a structure has alternate locations, you can get just the highest occupancy bonds/atoms with a.primaryBonds() and a.primaryNeighbors(). Molecules have a corresponding m.primaryAtoms() function. Residues have a simpified interface to their atoms: r.atoms() returns a list of atoms r.atomNames() returns a list of atom names r.atomsMap() is both of the above combined as a dictionary with atom name as the key and a list of atoms with that name as the value Residue ids (of type MolResId) no longer have an exposed str method: r.id.str() is now 'str(r.id)' or 'print r.id' MolResId, Point, Vector, and Xform now have copy constructors. You can make copies in the C++ style, 'xprime = Xform(x)', or in the Python style with the copy module or the __copy__ method. The following chimera module functions are now static methods: Atom_getIdatmInfoMap -> Atom.getIdatmInfoMap Camera_hasMode -> Camera.hasMode Camera_modes -> Camera.modes Color_list -> Color.list Color_lookup -> Color.lookup Color_remove** Element_bondLength -> Element.bondLength Element_bondRadius -> Element.bondRadius LODControl_get -> LODControl.get Material_list -> Material.list Material_lookup -> Material.lookup Material_remove** Mol2io_isBlankLine -> Mol2io.isBlankLine Mol2io_splitLine -> Mol2io.splitLine OGLFont_defaultFont -> OGLFont.defaultFont OGLFont_setDefaultFont -> OGLFont.setDefaultFont OpenModels_get -> OpenModels.get PDBio_addStandardResidue -> PDBio.addStandardResidue PDBio_bondLengthTolerance -> PDBio.bondLengthTolerance PDBio_removeStandardResidue -> PDBio.removeStandardResidue PDBio_setBondLengthTolerance -> PDBio.setBondLengthTolerance PDBio_standardResidue -> PDBio.standardResidue PixelMap_list -> PixelMap.list PixelMap_lookup -> PixelMap.lookup PixelMap_maxLength -> PixelMap.maxLength PixelMap_remove** PseudoBondMgr_mgr -> PseudoBondMgr.mgr Residue_getDefaultRibbonStyle -> Residue.getDefaultRibbonStyle RibbonResidueClass_classes -> RibbonResidueClass.classes RibbonResidueClass_deregisterClass -> RibbonResidueClass.deregisterClass RibbonResidueClass_registerClass -> RibbonResidueClass.registerClass RibbonXSection_circle -> RibbonXSection.circle RibbonXSection_line -> RibbonXSection.line RibbonXSection_square -> RibbonXSection.square Selectable_count -> Selectable.count Shader_list -> Shader.list Shader_lookup -> Shader.lookup Shader_remove** Spline_makeGeometryVector -> Spline.makeGeometryVector Texture_computeComponents -> Texture.computeComponents Texture_computeDimension -> Texture.computeDimension Texture_computeImageTypeBytes -> Texture.computeImageTypeBytes Texture_computeTarget -> Texture.computeTarget Texture_list -> Texture.list Texture_lookup -> Texture.lookup Texture_remove** TrackChanges_get -> TrackChanges.get Xform_coordFrame -> Xform.coordFrame Xform_identity -> Xform.identity Xform_lookAt -> Xform.lookAt Xform_rotation -> Xform.rotation Xform_translation -> Xform.translation Xform_xRotation -> Xform.xRotation Xform_xform -> Xform.xform Xform_yRotation -> Xform.yRotation Xform_zAlign -> Xform.zAlign Xform_zRotation -> Xform.zRotation ** Color_remove, Material_remove, PixelMap_remove, Shader_remove, and Texture_remove Unlike C++, Python can not have a method and a static method with the same name. So the static method versions have been excised from the Python layer.

1 0

Getting the selected elements
by Wolf Cochrane 06 Oct '05

06 Oct '05

Hi, I've written software and want to use Chimera as vector application for it. As a input step I want the user to select a atom on a structure, using his/her mouse in the Chimera GUI. I've had a look at the Chimera code and online documentation but haven't been able to figure out how to get the selected elements (Existing elements) on a structure. I will appreciate it if you can help me out. Regards Wolf Cochrane Bioinformatics and computational Biology Unit University Pretoria

2 1

accelerators and stereo
by Justin Wu 18 Aug '05

18 Aug '05

Hi Would you please let me know how to make a cross-eye figure from Chimera? I do not where to look for this function. Thanks Justin ************************************************ Justin Wu Rm 752, Biological Science Building 484 West 12th Ave, Columbus, OH 43210 Tel: (614)247-5040, Fax: (614)292-6773 ************************************************

2 1

3d File formats
by peter allen 05 Jul '05

05 Jul '05

Hello, Does your software have any way of exporting 3d file formats. DXF OBJ 3DS IGES STL DWG etc Many Thanks Peter Allen

2 1

Re: [chimera-dev] Source code availability
by Tom Ferrin 17 Jun '05

17 Jun '05

James, Ninty percent of Chimera is written in Python and that code is distributed in source-code form with our standard distribution. The remaining code is written in C++ primarily for efficiency considerations, especially for some of the low-level OpenGL graphics functionality. Tom Goddard is correct that we do not routinely distribute the C++ source, but we have no problem providing it to you on request. Please note, however, that we do not have the resources necessary to provide help to you in setting up the development environment necessary to successfully compile and link the C++ source and the multitude of other 3rd party packages that Chimera uses. Creating a full build-from-source copy of Chimera is a lot of work and depends on getting a bunch of things in the build environment just right. This, and the fact that the build-from-source procedures are not well documented, are the primary reasons we do not automatically include the C++ source in our standard distribution. But if you'd like a copy of the C++ source, we are happy to provide it. --tef --- Thomas Ferrin, PhD Professor of Pharmaceutical Chemistry and Biopharmaceutical Sciences Director, Resource for Biocomputing, Visualization, and Informatics University of California 600 16th Street, Rm N472 San Francisco, CA 94143-2240 Phone: 415-476-2299 Fax: 415-502-1755 Email: tef(a)cgl.ucsf.edu ------- Forwarded Message Date: Thu, 16 Jun 2005 10:55:54 -0700 From: Thomas Goddard <goddard(a)cgl.ucsf.edu> To: jjv5(a)nih.gov cc: chimera-dev(a)cgl.ucsf.edu Subject: Re: [chimera-dev] Source code availability Hi Jim, The Chimera C++ source code is available on request for outside developers. Most of the source code is Python which comes with all Chimera distributions. The Chimera C++ header files are also available. The link for those is in the Chimera Programmer's Manual (not on the download page). http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html The Chimera C++ source code is currently provided by request. The C++ source is not freely available for reasons I do not understand. You would need to discuss that with the head of our lab Tom Ferrin (tef(a)cgl.ucsf.edu) There is one piece of code used by Chimera for computing molecular surfaces (MSMS from Michel Sanner) for which the source code is not available. Chimera depends on 25 third party packages (TclTk Togl Tix Pmw PyOpenGL zlib Python Numeric jpeg tiff freetype Imaging netcdf Scientific MMTK HappyDoc tr openssl ftgl omni msms otf autostereo swish-e FFmpeg), so it is quite alot of work to compile it yourself. So the main use to you of the Chimera source code is probably for figuring out how Chimera works -- not for building it yourself. Tom _______________________________________________ Chimera-dev mailing list Chimera-dev(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev ------- End of Forwarded Message

1 0

Source code availability
by James Vincent 16 Jun '05

16 Jun '05

Hello, It appears full source code for Chimera is not available for download. The chief of our lab is reluctant to start an extension project without access to the full source. Is it available by request? Thanks, Jim ---- James J. Vincent, Ph.D. National Cancer Institute National Institutes of Health Laboratory of Molecular Biology Building 37, Room 5120 37 Convent Drive, MSC 4264 Bethesda, MD 20892 USA 301-451-8755 jjv5(a)nih.gov

2 1

solaris
by Marcos Oliveira de Carvalho 16 Jun '05

16 Jun '05

Hi, In first place, congratulation for the great software. Chimera is really very very nice. I want to ask if a solaris version is planned. If not, there are any place were I can find information on how to port it? (crucial files for porting, etc.) many thanks Marcos de Carvalho ---------------------------- Marcos Oliveira de Carvalho Structural and Functional Genomics Group www.genesul.lncc.br www.cbiot.ufrgs.br/~wwwgenoma

2 1

Xform for rotation about a point
by Thomas Goddard 08 Jun '05

08 Jun '05

> From: "Lavu Sridhar" <slavu(a)bcm.tmc.edu> > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Subject: Rotation about arbitrary point > Date: Tue, 7 Jun 2005 16:44:35 -0500 > > Hi, Tom, > > I want to rotate a chimera model about > an arbitrary point - (ax,ay,az). > > Basicallly, what I am looking for is > something like following: > > xform.rotate(axis, angle, about_point) > > Is that possible? > > Thank you. > > Lavu Hi Lavu, There is not an Xform constructor to rotate about a specified point although it would be nice and I'll suggest it to Greg Couch (gregc(a)cgl.ucsf.edu) who maintains the Xform code. Here is how you currently would create a rotation about a center (cx,cy,cz): >>> center = chimera.Vector(cx, cy, cz) >>> axis = chimera.Vector(ax, ay, az) >>> angle = 123.4 # in degrees >>> xf = chimera.Xform_translation(center) >>> xf.rotate(axis, angle) >>> xf.translate(-center) # To apply transform to point p to get rp use: >>> p = chimera.Point(px, py, pz) >>> rp = xf.apply(p) This transform acts on a point by first translating by (-cx,-cy,-cz) then rotating about axis (ax,ay,az) by angle, then translating back by (cx,cy,cz). That achieves the rotation you want about (cx,cy,cz). I'd suggest making a function to do this if you need it at several places in your code. Tom

1 0

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

2 1

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

2 1

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 ------- >

1 0

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())

1 0

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

1 0

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

2 1

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

2 1

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

3 3

[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

1 0

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

1 0

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

1 0

[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

2 1

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

2 1

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 -------

2 1

Material science feature requests
by Thomas Goddard 23 Oct '04

23 Oct '04

Here is email I exchanged with Chris Greenwell about using Chimera for a material science / molecular dynamics study. Tom --------- Date: Thu, 21 Oct 2004 09:14:55 +0100 Subject: Re: Material visualization with Chimera From: "H. Chris Greenwell" <h.greenwell(a)ucl.ac.uk> To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Hi Tom, First of all, Chimera is fantastic! Congratulations! Yes, I noticed the problem with large numbers of atoms. We run systems getting on for 500,000 atoms., but most are less than 100,000 atoms. I still use the Atom Eye software, which is more efficient at using memory (http://164.107.79.177/Archive/Graphics/A/) for large models. However, it is less intuitive to use and doesn't have much of the functionality that we would like. The type of work we do at the moment involves simulating the interlayer region of layered clay type structures with organic molecules, such as long monomers, between the crystalline clay sheets. We do this to gain insight into the interlayer arrangement and dynamics not attainable by experimental means. We have to present data which is both meaningful and interesting to the experimental community. We use the LAMMPS code as our large-scale MD engine, from Sandia. We have our own data analysis tools to generate RDFs, diffusion coefficients and atom density plots. However, in order to make sense of the features, and to spot unusual features that get averaged in the data of these numerical data sets it is necessary to visualize the model through the simulation. As an ex-experimental chemist I have a strong bias to the visual! I have looked at many types of software, and essentially we have two considerations: 1) A visualizer for looking at each frame, and movies of the atom positions. Data analysis as described above. 2) A builder for loading crystalline unit cells, generating organic monomers, translating, rotating and deleting atoms/molecules. Critically, we tend to use periodic boundary conditions in all our simulation so an ability to replicate unit cells and visualize the boundary markers when desired. Functionality to place forcefield atom types on the system is also needed. I have come across only two contenders to do this with: ECCE (http://ecce.emsl.pnl.gov/) looks promising and is free to academia, however, as with many freeware builders/visualizers, it is only for bio-systems and has no concept of periodic unit cells. I also am unaware of the atom number capability. Materials Studio/Cerius 2. These are the commercial options from Accelrys and work very well. Unfortunately, these are also incapable of building models greater then approx. 30,000 atoms for materials science. Materials Studio has a bug, which stops it doing this, and Cerius 2 (a) gets very slow, and (b) has a purely numeric atom numbering, which has a 5 digit capacity and relies on the molecules being made up of residues. We are starting to use the latest LAMMPS2003 software from Sandia, and may well look at steering it in the future, so any developments in Chimera to aid us in looking at materials would be much appreciated. Many thanks Chris On Thursday, October 21, 2004, at 12:02 AM, Thomas Goddard wrote: > Hi Chris, > > Dave Konerding told me you tried using Chimera to visualize materials > with large numbers of atoms. Unfortunately Chimera uses alot of memory > per atom (~2 Kbytes) and gets pretty slow for systems of 100,000 atoms > or more. > > I'm curious about what you are looking for with Chimera and whether > there are new features you would need. We primarily focus on proteins > and nucleic acids but would consider adding features to help in > materials > science. > > Tom Goddard > Chimera developer > UC San Francisco > > H. C. Greenwell EPSRC Fellow Centre for Computational Science Christopher Ingold Laboratories University College London 20 Gordon Street London WC1H 0AJ United Kingdom --------- Date: Thu, 21 Oct 2004 10:54:31 +0100 Subject: Chimera materials visualization wish list From: "H. Chris Greenwell" <h.greenwell(a)ucl.ac.uk> To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Hi Tom, I realise that in my earlier e-mail I have only outlined general points, and therefore have only addressed part of your email. Therefore, if I could compile an initial wish-list of new features (apologies if some of this is already in the code, as I am still getting to know it) it might look something like: 1) To be able to import the common file types we use in our simulations. These are: (a) the LAMMPS 2001 output files (.pos), which are largely XYZ files with a time step and an atom type number related to, (b) the LAMMPS 2001 data file (.dat/.lmp), which contains the atom information (masses), coordinates and bonding. (c) the LAMMPS 2003 data/position files, which I think are a little different but will be used by us in the near future. (d) the Accelrys Biosym coordinate (.car) file, topology (.mdf) file and trajectory (.arc/.trj) files. Dave kindly put together a little utility for the .car/.mdf file. 2) To be able to remap any atoms that have moved outside the cell, within the cell boundaries when visualized. 3) To be able to view the cell boundaries as a dashed/solid/no line. 4) To be able to replicate the viewed model in XYZ directions so that motion across cell boundaries can be followed. 5) To be able to turn the replicated unitcells into one supercell (we have an utility to do this with .car/.mdf) . 6) To be able to display and select atoms on the basis of forcefield atom types. 7) To be able to render crystalline structures as polyhedra. 8) After visualizing, or performing molecule/atom translations/deletions/insertions etc, to be able to export as the file types listed in (1) and also the Atom Eye (.cfg) format. Many thanks Chris H. C. Greenwell EPSRC Fellow Centre for Computational Science Christopher Ingold Laboratories University College London 20 Gordon Street London WC1H 0AJ United Kingdom

1 0

[chimera-dev] API change in next release: no more selection.selectionModels()
by Eric Pettersen 03 Oct '04

03 Oct '04

If you based any code off the "Selections" programmer's example, you may be using the selection.selectionModels() function to get a list of models to restrict selections to. That function is going away with the next release. You should use the chimera.openModels.list() function instead as explained in the revised example now on the Chimera web site. Using the openModels.list() function will work in 1.1951 and prior releases as well as our next release which should be out next week. At one point, it had been our intent to allow users to designate a set of models to restrict selections to, which was the raison d'etre for the selectionModels() function. The implementation of an interface designating such models never materialized and over time the whole mechanism just seemed to be unnecessary, so we are dropping the idea and the corresponding API baggage. I apologize for any inconvenience. Eric Pettersen UCSF Computer Grpahics Lab pett(a)cgl.ucsf.edu

1 0

proxy support
by Eric Pettersen 23 Sep '04

23 Sep '04

The development version of Chimera now has support for proxy web servers (controlled in the "Web Access" preferences category). Developers should try to use urllib.urlopen or urllib2.urlopen whenever possible rather than using httplib directly so that proxying will work without having to explicitly provide for it in your code. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 0