- Chimera-users - RBVI Mailing Lists

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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X11 updated for Mac OS X, stereo now?
by David Belnap 02 Nov '06

02 Nov '06

Apple has released an update for X11 with the following comment: This update addresses several issues in the X11 for Mac OS X package, enabling it to better handle: - GLX stereo visuals - offscreen rendering to GLX Pbuffers and Pixmaps I downloaded it and tried to run Chimera (beta version 1 build 2199 2006/01/24) in stereo. It didn't work. Does the X11 update have the stereo-in-a-window capability now that Chimera needs? Is there a newer version of Chimera that will run in stereo on the Mac? David ============================================ David M. Belnap Department of Chemistry and Biochemistry Brigham Young University Provo, Utah 84602 USA Phone: 801-422-9163 FAX: 801-422-0153 David_Belnap(a)byu.edu ============================================

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Re: [Chimera-users] Chimera length units
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, Chimera clipping and other tools use xyz coordinates and do not use voxel or pixel measures. The volume dialog region bounds panel and the volume dialog step size are exceptions where voxel index positions are used. The notion of a voxel is only relevant to density maps, not atomic models and clippping applies to all kinds of data, not just maps. Screen pixels are a 2 dimensional concept so it is an awkward measure to use especially with perspective 3-d viewing for measuring lengths. Tom > From: Jeff > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Subject: RE: Chimera length units > Date: Thu, 2 Nov 2006 14:30:30 -0800 > > does this mean that I can't refer to a given coordinate by pixel/voxel > location without resetting the voxel size to '1 1 1' (which I might not want > to do - does chimera not keep the mrc file (or other voxel data) inside of a > similar kind of array) > > > -----Original Message----- > > From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] > > Sent: Thursday, November 02, 2006 1:46 PM > > Cc: chimera-users(a)cgl.ucsf.edu > > Subject: Chimera length units > > > > > > Hi Jeff, > > > > Chimera does not know what units you are using, the data > > coordinates are just numbers as far as it is concerned. If > > you open a PDB atomic model the coordinates are always > > Angstroms. If you open a density map, say an MRC file, the > > header may include the voxel size. That value could be in > > Angstroms or nanometers. Often maps don't have the true > > voxel size in the header, often they say it is 1. In such > > cases you can use the Chimera volume dialog menu entry > > "Features / Origin and Scale" to set the voxel size in > > Angstroms or nanometers so that the map can be aligned with > > other models or maps. If you open a PDB model in Angstroms > > and a map with the scale set in nanometers then the map will > > look 10 times smaller than it should be relative to the model. > > > > Tom

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Chimera length units
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, Chimera does not know what units you are using, the data coordinates are just numbers as far as it is concerned. If you open a PDB atomic model the coordinates are always Angstroms. If you open a density map, say an MRC file, the header may include the voxel size. That value could be in Angstroms or nanometers. Often maps don't have the true voxel size in the header, often they say it is 1. In such cases you can use the Chimera volume dialog menu entry "Features / Origin and Scale" to set the voxel size in Angstroms or nanometers so that the map can be aligned with other models or maps. If you open a PDB model in Angstroms and a map with the scale set in nanometers then the map will look 10 times smaller than it should be relative to the model. Tom > From: Jeff > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Date: Thu, 2 Nov 2006 13:26:11 -0800 > > thanks Tom, > > sorry for a goofy question, but how do I know what units chimera is using > (for measuring distances, having the output is nice in Angstroms, but > sometimes (like with orienting a clipping plane) using unitless/pixels is > more handy for displacements/etc) > > thanks, > > -jeff

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Per-model clipping plane command
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, There isn't yet a Chimera command for per-model clipping. Below is some Python code that can do it. Open a density map and then open this Python code in Chimera to clip it. Some more code can make it loop through different depths. There is some trickiness to making it update the graphics window in such a loop. Ask for details if you want that. Tom > From: Jeff > To: <goddard(a)cgl.ucsf.edu> > Subject: per-model clipping plane question (or similar) > Date: Thu, 2 Nov 2006 10:54:26 -0800 > > hi Tom, > > was wondering if I can control the per-model clipping plane > orientation/parameters/etc via command line or shortcuts - > > would like to be able to methodically push a clipping plane in 'slab mode' > through my model to compare it w/ other 2D/projection tools I use - I know I > can click 'orient' on the model and it will orient to a default > position/rotation (and I can click orient on the per-model clipping plane > and therefore register them both), but is there then a way that I can > specify (say, along one axis, like z) where the slab/clipping plane is > positioned, like in pixels? > > can I control the angular position of the clipping plane via command line, > too? > > thanks, > > Jeff ----- Python code clip.py. # ----------------------------------------------------------------------------- # Python function to control per-model clipping (like menu entry # Tools / Depiction / Per-Model Clipping). The clip plane rotates with # the model (PDB structure, density map, ...). # # Parameters: # model is a Chimera Model # origin is (x,y,z) of point on clip plane. # normal is (nx,ny,nz) pointing towards clipped (invisible) half of plane. # slab_thickness is in data length units (usually Angstroms). # # Origin and normal are relative to the data coordinate system, for example, # the x,y,z coordinates of a PDB atoms or axes of a density map. The clip # def set_clipping(model, origin, normal, slab_thickness = None): p = model.clipPlane from chimera import Point, Vector p.origin = Point(*origin) p.normal = Vector(*normal) model.clipPlane = p model.useClipPlane = True if slab_thickness == None: model.useClipThickness = False else: model.clipThickness = slab_thickness model.useClipThickness = True # ----------------------------------------------------------------------------- # Cap holes left when clipping a surface. Controls graphical interface # shown by menu entry Tools / Depiction / Surface Capping. # # Parameters: # cap_color is (r,g,b) or (r,g,b,a) where values in range 0-1 # cap_mesh is True or False for mesh or solid cap appearance # cap_subdivision of 2 makes cap mesh twice as fine for detailed coloring. # cap_offset in data length units (usually Angstroms) for large models # sometimes needs to be larger to avoid cap itself being clipped due to # finite floating point precision in OpenGL. # def show_surface_caps(show, cap_color = None, cap_mesh = False, cap_subdivision = 1, cap_offset = 0.001): from SurfaceCap.gui import capper_dialog d = capper_dialog(create = True) d.Close() use_color = (cap_color != None) if use_color: d.use_cap_color.set(use_color) d.cap_color.showColor(cap_color) if cap_mesh: d.cap_style.set('mesh') else: d.cap_style.set('solid') d.subdivision_factor.set(cap_subdivision) d.cap_offset.set(cap_offset) d.show_caps.set(show) # ----------------------------------------------------------------------------- # Example using set_clipping(). # from chimera import openModels mlist = openModels.list() m = mlist[0] set_clipping(m, (.5,0,1), (0,1,1), 8) show_surface_caps(True, (1,0,0), True) # Red mesh caps

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Chimera under FreeBSD
by Devon Ryan 01 Nov '06

01 Nov '06

Has anyone had success getting chimera to run under FreeBSD? I can get the linux version to start (under the linuxulator), but it crashes after ~20 seconds when the bundled version of python core dumps. I'm running FreeBSD 6.1 on an intel architecture. Thanks -- Devon Ryan | dpryan(a)sg.uchicago.edu Neuro Grad Student, Ptacek Lab | dpryan(a)phy.ucsf.edu University of Chicago '02 | dpryan(a)alumni.uchicago.edu www.dpryan.com | dpryan(a)dpryan.com ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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question regarding chimera 1.2304-wim32.exe
by AJ Campbell 31 Oct '06

31 Oct '06

I have tried installing Chimera several times on my Windows machine but keep receiving an error message saying "Outline highlight not supported by hardware", any advice would be appreciated. ~ Arthur

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atom name balloons
by Greg Pintilie 31 Oct '06

31 Oct '06

I was wondering why in the new release of Chimera ballons no longer pop up when the mouse is placed over an atom and is left there... is this an option that has to be set somewhere? I found it extremely usefull and now am missing it... Greg

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problems with starting Chimera
by Mareike Goeritz 30 Oct '06

30 Oct '06

Hello, I'm interested in using Chimera, but after downloading and installing the software I'm unable to launch the program. I always get the following error message: "Microsoft Visual C++ Runtime Library: Assertion failed! Program: C:\Program Files\Chimera\bin\pythonw.exe File: togl.c Line: 2994 Expression: res==TRUE For information on how your program can cause an assertion failure, see the Visual C++ documentation on asserts (Press Retry to debug the application - JIT must be enabled)" I'm not familiar with C++, so I don't know what to do. Does anybody know what might be missing or what's the problem? Thank you for your help!! Mareike -- ******************************** Dr. Mareike Goeritz Department of Chemistry, MC 164-30 California Institute of Technology 1200 E. California Blvd. Pasadena, CA 91125 (626) 395-6032 Tel (626) 683-8753 Fax goeritz(a)caltech.edu ********************************

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