Hi Francesco and others, People with MD trajectories can also use this new EnsembleCluster tool (available in the most recent daily builds) by: - viewing the whole trajectory with the "MD Movie" tool, or at least all the frames you want to cluster - from the MD Movie dialog menu, choosing File... Save PDB and saving "all frames" to a file - quitting from MD Movie and opening the new file with File... Open - choosing Tools... MD/Ensemble Analysis... EnsembleCluster, clicking the line that shows that new file, then OK I just tried this to make sure it works. The clustering calculation may take a while, but eventually another dialog with results should appear. This tool is still under development and may change, but this will at least allow users to try it on trajectory ensembles as well as NMR ensembles. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@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
Hi, I'm pretty newbie for Chimera. Anyone knows there is a function to display a density map as a gradient map? My purpose is: - Having one density map displayed as a surface rendering map - Having another different density map displayed as a gradient map only on the surface of the surface rendering map above. Thanks a lot, Huy
Hi Huy, If I understand correctly, you want (1) a isosurface of the density map (2) colored by the gradient in that same map. (1) If you open the density map in Chimera, it will automatically start Volume Viewer, in which you can adjust the isosurface display (contour level(s), smoothing, etc.). More details on Volume Viewer: http://www.cgl.ucsf.edu/home/meng/docs/ContributedSoftware/ volumeviewer/framevolumeviewer.html (2) Then you can use Surface Color (listed under Tools... Volume Data in the main menu, or in the Volume Viewer Tools menu) to color that isosurface by the data gradient. You do not have to make a separate map with the gradient. In Surface Color, choose the option to use the "gradient norm" of the density map you already opened. Then you can adjust how colors should map to the gradient norm values. More details on Surface Color: http://www.cgl.ucsf.edu/home/meng/docs/ContributedSoftware/surfcolor/ surfcolor.html I hope this is what you had in mind. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@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 Dec 21, 2007, at 12:49 AM, Bui Khanh Huy wrote:
Hi, I'm pretty newbie for Chimera. Anyone knows there is a function to display a density map as a gradient map?
My purpose is: - Having one density map displayed as a surface rendering map - Having another different density map displayed as a gradient map only on the surface of the surface rendering map above.
Thanks a lot, Huy
Hi Elaine, I tried what you told me, and it seems to work like what I expected. But I just want to confirm what I did is right as I don't fully understand the guide on the webpage you gave me. My question: I have volume A & B. I want to color the surface of volume A by the gradient of volume B. What I did: - I chose iso surface display of volume A using Volume Viewer. - Go to Tools/Volume Data/Surface Color, choose Color Surface A, using B gradient norm, then Color. Best regards, Huy ________________________________ Von: Elaine Meng [mailto:meng@cgl.ucsf.edu] Gesendet: Fr 12/21/2007 4:54 An: Bui Khanh Huy Cc: chimera-users@cgl.ucsf.edu Betreff: Re: [Chimera-users] Gradient map Hi Huy, If I understand correctly, you want (1) a isosurface of the density map (2) colored by the gradient in that same map. (1) If you open the density map in Chimera, it will automatically start Volume Viewer, in which you can adjust the isosurface display (contour level(s), smoothing, etc.). More details on Volume Viewer: http://www.cgl.ucsf.edu/home/meng/docs/ContributedSoftware/ volumeviewer/framevolumeviewer.html (2) Then you can use Surface Color (listed under Tools... Volume Data in the main menu, or in the Volume Viewer Tools menu) to color that isosurface by the data gradient. You do not have to make a separate map with the gradient. In Surface Color, choose the option to use the "gradient norm" of the density map you already opened. Then you can adjust how colors should map to the gradient norm values. More details on Surface Color: http://www.cgl.ucsf.edu/home/meng/docs/ContributedSoftware/surfcolor/ surfcolor.html I hope this is what you had in mind. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@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 Dec 21, 2007, at 12:49 AM, Bui Khanh Huy wrote:
Hi, I'm pretty newbie for Chimera. Anyone knows there is a function to display a density map as a gradient map?
My purpose is: - Having one density map displayed as a surface rendering map - Having another different density map displayed as a gradient map only on the surface of the surface rendering map above.
Thanks a lot, Huy
Hi Huy, It sounds like you did exactly the right thing. The description in my previous message was slightly different because I thought you wanted the surface and gradient both from the same volume data. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@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 Dec 24, 2007, at 3:29 PM, Bui Khanh Huy wrote:
Hi Elaine,
I tried what you told me, and it seems to work like what I expected. But I just want to confirm what I did is right as I don't fully understand the guide on the webpage you gave me.
My question: I have volume A & B. I want to color the surface of volume A by the gradient of volume B.
What I did: - I chose iso surface display of volume A using Volume Viewer. - Go to Tools/Volume Data/Surface Color, choose Color Surface A, using B gradient norm, then Color.
Best regards, Huy
participants (2)
-
Bui Khanh Huy -
Elaine Meng