- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] opacity for stick representation in chimera
by Elaine Meng 12 Feb '07

12 Feb '07

Hi Jerome, First make a transparent color and then use it on the atoms/bonds - there are a handful of routes. You can make the transparent color using the Color Editor (under Tools... Utilities; click the Opacity to get a slider for that, then adjust the red/green/blue/opacity sliders as desired). This color can be used on atoms/bonds, ribbons, whatever (depending on the current target setting under Actions.. Color) by choosing "Actions... Color... from editor" or it can be used in coloring commands using the color name "fromeditor" Color Editor description: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortool.html Alternatively, you can make the transparent color with the command "colordef" and give it whatever name you want. The new color name can then be used in coloring commands. Color definitions are saved in sessions. Or, if you don't want to save sessions, just make a command file with all of your favorite color definitions and read it in whenever you want those colors defined. "colordef" man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/colordef.html I hope this makes sense - feel free to write back if it doesn't! Best, E ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Feb 11, 2007, at 5:14 PM, Jerome Nilmeier wrote: > Hi Elaine: > > I was wondering: can you adjust the opacity of the stick > representation in chimera? > > best, J

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xforms, cpk scale
by Randy Heiland 08 Feb '07

08 Feb '07

Is there a command to scale sphere of a CPK rep? Is there a command to save the current viewing transformation to a file and then read it back/apply it at a later time? Thanks, Randy

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Drawing Artifacts
by Albion Baucom 08 Feb '07

08 Feb '07

Using the latest stable current production release of Chimera, 1.2304, I have begun to experience some drawing problems that I never had in previous versions. Specifically I frequently get a thin wireframe rendering of my protein structure when I draw the structure as a ribbon with a volume open at the same time. This wire frame persists even when I turn the display of the molecule off in the model panel, and it also does not rotate or translate if the protein is selected as the only active object. In effect it leaves behind a ghost image. Curiously this representation alternates from a light gray/white color to black when I open dialog boxes. The artifact toggles on and off with the volume in some instances. My processing and graphics hardware have not changed recently, nor has operating system (Linux). I do not experience this behavior with my last version of Chimera, 1.2199; it never renders this artifact. I have a nVidia Geforce 6800GT graphics card with the nVidia Linux drivers 1.0-9746. My X11 server is version 6.8.2. Here is a screen image of this phenomenon http://msg.ucsf.edu:8100/~baucom/images/chimera_image.jpg I have rotate the model slightly to show that the thin wireframe stays behind. It is not a separate object in the model panel. Thanks Albion

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Morph Map
by Tom Goddard 08 Feb '07

08 Feb '07

I've added a Chimera extension called Morph Map http://www.cgl.ucsf.edu/chimera/experimental/morph_map/morphmap.html to the experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html It interpolates between two volume data sets and makes animations. The original version of this tool was written by Wei Zhang in Pawel Penczek's lab. Tom

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Re: [Chimera-users] Map Orientation for Symmetry Plug-in
by Tom Goddard 07 Feb '07

07 Feb '07

Hi Albion, Ok, I made the "fit map in map" tool print out a point on the rotation axis. The new code for use with Chimera 1.2318 is here: https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=experimental/fitmap231… The zip file contains a directory FitMap that you put in your Chimera distribution under chimera/share or on Mac Chimera.app/Contents/Resources/share For more installation details see http://www.cgl.ucsf.edu/chimera/experimental/install.html This FitMap directory replaces your existing one. After restarting Chimera you can fit a helically symmetric map in a rotated copy of itself then get the axis point (shown in Favorites / Reply Log) and adjust the map origin (volume dialog Features / Origin and Scale) to put the axis point at (0,0,0). I described this in more detail in my previous message: http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001313.html The output of the axis point will be included in the next Chimera snapshot due out in one to three weeks. The matrix you sent me had no rotation, just a translation by 52 along z. You will need to rotate the map copy before fitting to get a meaningful rotation axis point. In fact I suspect the accuracy will be increased for rotations near 180 degrees rather than small rotations (e.g. 30 degrees). Tom Albion Baucom wrote: > Thanks Tom. > > OK, here is my rotation matrix after following your instructions > > 0.99944468 -0.03326699 0.00190528 -0.09024247 > 0.03326443 0.99944566 0.00136109 0.10539160 > -0.00194951 -0.00129696 0.99999726 52.82194789 > > Sorry, I forgot how to compute the rotation axis vector from this > matrix ... its been awhile since I had to do that manually ... its > pretty simple if I remember right. > > Any code to automate this would be greatly appreciated. > > Thanks again! > > Albion

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colorzone tool
by Jeff 07 Feb '07

07 Feb '07

would it be possible to allow 'color zone' to go past 30 A radius? -Jeff

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Hiding part of a marker set
by Tom Goddard 07 Feb '07

07 Feb '07

Hi Jeff, You can hide part of a marker set by selecting the markers you want to show (maybe using the select connected shortcut "sc" as described earlier) then use invert selection (main window menu Select / Invert, or shortcut "is"), then use path tracer menu entry Actions / Hide markers (or shortcut "ha" for hide atoms). Tom Jeff wrote: > I don't suppose there's a way to hide only a portion of a marker set > (just keep one filament visible out of 10, for instance) > > -Jeff

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Mac laptop benchmark
by Tom Goddard 07 Feb '07

07 Feb '07

Hi Jeff, I ran the Chimera benchmark tool on my new MacBook Pro and got scores: surface 543 mesh 545 contour 183 solid 256 recolor 132 But running hand tests I see the real surface/mesh scores should be 380. It appears the benchmark no longer is reporting correct scores either because a graphics driver optimization is speeding things up because the test image is not actually displayed, or Chimera code has changed (perhaps no longer guaranteeing the OpenGL buffers are swapped). Probably other scores on the Chimera benchmark web page are likewise inaccurate. This will have to be investigated. At any rate, actual surface rendering is about 65% faster than my Dell Precision M50. A test on a GeForce Go 7400 (aka Quadro NVS 120M) in a new Dell Lattitude D820 also gave erroneous scores, but hand testing gave surface rendering score 420 and horrible mesh (110) and solid (<20) numbers. Tom Jeff wrote: > could you run the benchmark on your mac? (I have run it on my > workstation, but forgot the scores; will do again and compare) > > -jeff

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NumPy in Chimera
by Tom Goddard 07 Feb '07

07 Feb '07

Hi Chimera Extension Writers, If you have written Chimera extensions that use Numeric Python you will need to convert them to instead use NumPy to work with future versions of Chimera. NumPy provides almost all the same routines as Numeric but some function and module names have changed. We are switching Chimera over from Numeric Python to NumPy and will have a Chimera snapshot out in one to three weeks that uses NumPy. We envision having a Chimera production release that uses NumPy in perhaps 3 months. The change was necessary because Numeric is no longer maintained. Numeric will no longer be included with Chimera because dynamic library name space collisions with NumPy occur on the Mac because of certain Chimera compilation options. The conversion of Chimera code was not much trouble, but we had to also convert third party packages that are included with Chimera (PyOpenGL, MMTK, Scientific (for netcdf file reading), MSMS molecular surfaces) and that took some work. Thanks for your patience. Tom

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Re: [Chimera-users] question about mac laptops / workstations and chimera stability
by Tom Goddard 06 Feb '07

06 Feb '07

Hi Jeff, I just got my MacBook Pro with 2 Gb memory and 160 Gb hard-drive yesterday. It's been working well with Chimera volume display, surface and solid. Performance is roughly a factor of two better than my 4 year old Dell Precision M50 with Quadro 4 GoGL 500 graphics (a very heavy machine, ~10lb). I just took a look at a 2k by 2k by 76 tomogram and performance was as expected. 2 Gb memory is adequate for my uses. I went for the 160 Gb harddrive instead of the 120 Gb since volume data and video can take some space. The 200 Gb option was a 4200 rpm drive which I suspect would be slower than the smaller 5200 rpm models so I avoided it. If you'd like to try my laptop before you order you are welcome to come over to my house in SF. Tom Jeff wrote: > Tom, > > is the base 2 GB memory sufficient, and do you have any reservations > regarding transfer speed from the harddrive? > > I am going to place an order, wanted to check with you first about > those 2 things before going ahead. > > (I figure, if you are developing on it, this is not a bad idea.) > > -Jeff

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