- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] SEPARATING A SUBUNIT
by skmolugu＠miners.utep.edu 29 Sep '08

29 Sep '08

Hi, I have a CryoEM density map with 14 subunits with seven fold symmetry. Is there a way in chimera to separate only one subunit from the entire map. thanks, sudheer

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Calculating RMSD for ligand
by 吴超 27 Sep '08

27 Sep '08

Hi, dear folks, I want to evaluate the docking performance by calculating the RMSD of heavy atoms between ligand crystal conformation and docked conformation. I use the following command: rmsd #0:1.het & ~element.H #1:1.het & ~element.H But Chimera seems to forget the correct order and give a pairwise alignment not the way I want . I wonder if there is a way that I can get the correct selection order so as to calculate RMSD. Best -- Chao Wu Currently: National Institute of Biological Sciences, Beijing Huang Niu's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206

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calculating symmetry for a dimer structure
by Katryna Cisek 26 Sep '08

26 Sep '08

Hi, Is there a way of calculating symmetry for a dimer structure in chimera, e.g. axis of symmetry? Thanks, Katryna

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calculating symmetry for a dimer structure
by Katryna Cisek 26 Sep '08

26 Sep '08

Hi, Is there a way of calculating symmetry for a dimer structure in chimera, e.g. axis of symmetry? Thanks, Katryna

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error in vista
by Mugnaioli, Enrico 25 Sep '08

25 Sep '08

Dear Chimera Users, I installed Chimera in my new PC, working under Vista. Apparently, the installation was fine, but when I started the program I got this error. What can I do? Best regards, Enrico Mugnaioli

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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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