Hi! Thanks so much for adding the define plane and define centroid features. Is there any way to add the option of defining the border of the plane as a polygon where the selected atoms define the polygon vertices? This would allow a plane in the shape of a hexagon or any other heterocycle to be inset inside of an aromatic ring for example without the edges of the plane being visible outside the bond enclosed area. Also, the thermal ellipsoid feature looks fantastic, however the probability setting doesn't seem to be functioning. Thanks again for adding all these features, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno@mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------
Hi Dave, If you just want to fill rings, use the "fillring" command: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fillring.html> or you can create arbitrary polygons with BILD format: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> The reason to use planes from Axes/Planes/Centroids is that they are "smart" objects that can be used in distance and angle measurements with atoms, axes, and centroids, as alluded to in my other replies today. If display is all you are concerned with, either of these other methods will suffice. In Thermal Ellipsoids, the probability is working fine for me. You enter a number in the probability area and press return, which will accordingly adjust the number shown in the "Scale factor" field. Then that scale factor will be used the next time you click "Show Ellipsoids" or choose one of the Thermal Ellipsoid presets. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/thermal/thermal.htm...
I hope this helps, 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 Feb 20, 2010, at 7:07 AM, David Chenoweth wrote:
Hi! Thanks so much for adding the define plane and define centroid features. Is there any way to add the option of defining the border of the plane as a polygon where the selected atoms define the polygon vertices? This would allow a plane in the shape of a hexagon or any other heterocycle to be inset inside of an aromatic ring for example without the edges of the plane being visible outside the bond enclosed area. Also, the thermal ellipsoid feature looks fantastic, however the probability setting doesn't seem to be functioning.
Thanks again for adding all these features, Dave
Hi Elaine, Thanks for the help! Everything works fine now, I just forgot to hit enter after entering the probability. I was also wondering if the ring fill color and transparency be changed independent of the rest of the molecule? Thanks again, Dave On Feb 20, 2010, at 1:26 PM, Elaine Meng wrote:
Hi Dave, If you just want to fill rings, use the "fillring" command: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fillring.html>
or you can create arbitrary polygons with BILD format: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html>
The reason to use planes from Axes/Planes/Centroids is that they are "smart" objects that can be used in distance and angle measurements with atoms, axes, and centroids, as alluded to in my other replies today. If display is all you are concerned with, either of these other methods will suffice.
In Thermal Ellipsoids, the probability is working fine for me. You enter a number in the probability area and press return, which will accordingly adjust the number shown in the "Scale factor" field. Then that scale factor will be used the next time you click "Show Ellipsoids" or choose one of the Thermal Ellipsoid presets. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/thermal/thermal.htm...
I hope this helps, 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 Feb 20, 2010, at 7:07 AM, David Chenoweth wrote:
Hi! Thanks so much for adding the define plane and define centroid features. Is there any way to add the option of defining the border of the plane as a polygon where the selected atoms define the polygon vertices? This would allow a plane in the shape of a hexagon or any other heterocycle to be inset inside of an aromatic ring for example without the edges of the plane being visible outside the bond enclosed area. Also, the thermal ellipsoid feature looks fantastic, however the probability setting doesn't seem to be functioning.
Thanks again for adding all these features, Dave
Hi Dave, You're welcome! The ring fill automatically tracks the color/transparency of the ring atoms, but you can be wily and make it appear to be independent by opening two copies of the structure and using one copy for the desired fill color/transparency, as suggested in this earlier post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-August/ 004162.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 22, 2010, at 12:20 PM, David Chenoweth wrote:
Hi Elaine, Thanks for the help! Everything works fine now, I just forgot to hit enter after entering the probability. I was also wondering if the ring fill color and transparency be changed independent of the rest of the molecule? Thanks again, Dave
participants (2)
-
David Chenoweth -
Elaine Meng