On May 20, 2008, at 10:21 PM, Damien Larivière wrote:
Dear Elaine, Here is what I would like to do with Chimera :
From Tools/Structure analysis/sequence, it is possible to copy a portion of the aminoacid sequence of a protein and then to highlight in an other color this portion of sequence in a high resolution surface model (Actions / surface / show).
I would like to highlight a given portion of sequence but in a low resolution surface model. I tried High-Order Structure / Multiscale models with no success.
Thanks for you help and congratulations for the work you perform. Damien ------------------------------------------ Damien Larivière Fourmentin-Guilbert Scientific Foundation 2 Av. du Pavé Neuf, 93160 Noisy-le-Grand, France Phone : + 33 1 43 03 06 20 Cell phone : +33 6 82 19 81 32 damien.lariviere@fourmentinguilbert.org
Hi Damien, You can color a low-resolution surface for certain residues, but it takes an additional step as compared to coloring the high-resolution surface. Another difference is that it is done by distance cutoff, because it is no longer clear exactly which atom goes with which point on the surface. (1) First create the low-resolution surface. I can think of two different ways: (a) Multiscale Models - click "Make Models" and that will create a separate low-res surface for each chain. In that dialog, if you select "All" chains you can then edit the resolution value for those surfaces. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/ framemulti.html (b) command "molmap" - it makes a density map from the atomic coordinates, which you can then display as an isosurface. The Volume Viewer tool is automatically opened to show the density; in that tool, you can drag a bar on the histogram to change the contour level. In this case, all the atoms in the structure are used, and so you would get one "blob" (depending on contour level, though) rather than separate surfaces per chain. Volume Viewer has many additional options including surface smoothing (see Features... Surface and Mesh options). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/ framevolumeviewer.html (2) Select the residues and perform the coloring. This can be done exactly the same as for the high-resolution surface, and there are many different ways. To select the residues, you can use the Sequence tool (as you described), or the Select menu, or commands; to perform the coloring, you can use Actions...Color or the "color" command. However, the low-res surface will not be colored yet... (3) Use Color Zone (under Tools.... Volume Data) to color the surface to match the atoms you just colored. This just uses a simple distance cutoff and colors parts of the surface to match the closest atoms. After clicking Color, you can just drag the slider to change the distance cutoff. You're welcome! I hope this helps, Elaine P.S. we are working on better integration of different kinds of surfaces, so this procedure may change in the future ----- 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