- Chimera-users - RBVI Mailing Lists

adding H
by Barbara Truitt 25 Sep '08

25 Sep '08

I have a compound which has an imidazole ring. When I Add Hydrogens, no hydrogens are added to the nitrogen atoms when I use the build from 9/21/08. The build from 9/4/08 adds the hydrogens, but some of the charge assignments in the resulting mol2 file don't make sense. Barb Truitt

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Re: [Chimera-users] Creating and visualizing a plane
by Elaine Meng 24 Sep '08

24 Sep '08

On Sep 24, 2008, at 12:29 PM, Monica Tello wrote: > I found this very useful, thanks! > I have been trying to do a similar thing but creating a sphere to > put it surrounding the residues in the active site. I tried to > create a big water molecule, and this made the trick until I was > stuck because I can't change its transparency. Then I thought about > creating a marker such as you described for the plane, but I am not > familiar with creating these marker files and I am probably missing > commands in the .cmm file, because Chimera can't open the file and > is giving an error with the info written in it. > Could you help me out with it? Hi Monica, A marker is really just an atom, so that wouldn't make a difference. Normally you would use "Volume Tracer" (under Tools... Volume Data) to create the marker interactively with the mouse and then save it as a file from that tool instead of creating the file with a text-editor. I only edited the file in my example so I could specify the coordinates exactly. In fact, I created 3 markers interactively, saved the marker file from Volume Tracer, and then just edited the x,y,z coordinate values. You can make an atom/marker transparent by creating a transparent color and then using it (for example, choosing Tools... Utilities... Color Editor, clicking Opacity to include a transparency slider, creating the color, and using "colorpanel" as the color name in a command or "Actions... Color... from editor" in the menu). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortool.html> You can also create and name transparent colors with the "colordef" command: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/colordef.html> Show the atom in the sphere representation; you can change its radius, for example by selecting the atom and using a command something like: vdwdef 5.0 sel <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html> In fact, the "Volume Eraser" tool (under Tools... Volume Data) just makes a big transparent marker and its dialog has convenient controls for changing its color, radius, and position, so you might want to try that instead: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/volerase… > Yet another possibility is to make a spherical surface instead of an atom/marker. This can be done with the command "shape": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html> You can move that spherical surface relative to your structure and change its color just as described for the planar surface in my earlier message to Jim. I hope this helps, Elaine ----- 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

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Unable to turn reset multisampling. Graphics hardware supports request, but can not switch while maintaining display data.
by Andy LiWang 24 Sep '08

24 Sep '08

Dear Chimera, I just installed Chimera on my Dell XPS 1210 laptop (Windows Vista; Mobile Intel(R) 945GM Express Chipset Family). I get the following error everytime I start Chimera: Unable to turn reset multisampling. Graphics hardware supports request, but can not switch while maintaining display data. Molecules are not properly rendered and does not hide objects rotated behind other objects. I.e., some object appear in front regardless of rotation. This is a new problem. Chimera used to work fine on this computer. However, recently, I had Windows Vista reinstalled. Since the reinstallation, Chimera has these new problems. Any ideas? Thanks, Andy -- Associate Professor School of Natural Sciences UC Merced Atwater, CA 95301 Tel: (209) 228-4617 Fax: (209) 724-4356

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Re: [Chimera-users] Generating random helix
by skmolugu＠miners.utep.edu 24 Sep '08

24 Sep '08

Dear Chimera team, Is there any option in chimera that builds helix in a map at a position that is assumed to be a helix. thanks, sudheer

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Out of topic for Elaine
by Francesco Pietra 24 Sep '08

24 Sep '08

Hi Elaine: Although out of topic, as the author of the program "grid" you could be in the best position to give me general advice. Selecting spheres for only a portion of the protein failed to execute "grid" (at 0.3A grid_spacing) in a reasonable time. I choose this route in the hope to be able to examine docking (DOCK6) for the various parts of the molecule, in order to have the whole. I believe to have good reasons to do that. Is that what one should expect or does it mean that I did something wrongly? Thanks francesco pietra

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Movie recording
by Ibrahim Moustafa 24 Sep '08

24 Sep '08

Dear Chimera team, I have a problem with making a movie of morphed conformations in chimera (only for chimera 1.2548 installed on my laptop running XP). After doing the ³morph² when trying to record the movie I got the following error message: ³Error stopping/encoding movie: MidasError: Keyword and¹ does not match any known keywords² I don¹t understand the error message and what does it mean by ³keyword and²? I¹m not running a script. I don¹t have this problem with the Mac version of Chimera. The funny thing is that I was able to create a movie on the windows version a week ago. I¹m not sure if this problem has relation with XP and perhaps some new updates! Any idea how to solve this problem? many thanks for your great help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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Creating and visualizing a plane
by James Nettles 23 Sep '08

23 Sep '08

I'm not sure if this is a function available in Chimera. I have a protein system with three residues which define a plane, or floor, relative to an active site. I would like to display a translucent plane passing through the alpha carbon of these three residues to shoot an image. Further, I would like to quantify deviation of mobile regions relative to this plane. Thanks, Jim ________________________________________________________ James Nettles, Ph. D. Assistant Professor Department of Pediatrics, Emory University School of Medicine ________________________________________________________

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Scale_bar Gradient Color
by Anindito Sen 22 Sep '08

22 Sep '08

Hi All A simple question- How do I color the scale bar (in a gradient form). Also Has anyone experienced the problem of scale bar giving an incorrect measurement when a density map in .dat format is displayed in Chimera? Best Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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Show position in volume
by Magnus Gedda 22 Sep '08

22 Sep '08

Hello, I'm quite new to Chimera and have a small but annoying problem. I can place a marker in the volume and move it around, but I cannot find a way to see the xyz coordinate of the marker. How do I do this? Is there any other way to find out the xyz coordinates of a position in the volume? Best regards, Magnus

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VRML scene
by Eduardo Sanz García 19 Sep '08

19 Sep '08

Is it possible to export a VRML scene of only what it is been displayed in the window instead of the whole model? I wasn't able to open in chimera X3D files exported with chimera itself. Does chimera only writes but not read X3D files? Thank you.

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