- Chimera-users - RBVI Mailing Lists

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

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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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