Combining ribbons and ball-n-stick using neon
Dear Chimera- Wondering if there is a way to combine ball-n-stick rendered with neon and displaying distances as dashed lines with ribbons for other parts of the protein. I have attached an image captured with save, all looks good except the distances are not displayed as black lines because it has not gone through neon. If I run neon the ribbons do not show up. I would like to have both in the final image. Warmest regards, TOdd -- Todd M. Weaver, Ph.D. UW-La Crosse 1725 State Street Chemistry Department 4020 Cowley Hall La Crosse, WI 54601 Ph. (608)785-8269 Fax (608)785-8281
On Mar 8, 2005, at 3:07 PM, Todd Weaver wrote:
Wondering if there is a way to combine ball-n-stick rendered with neon and displaying distances as dashed lines with ribbons for other parts of the protein. I have attached an image captured with save, all looks good except the distances are not displayed as black lines because it has not gone through neon. If I run neon the ribbons do not show up. I would like to have both in the final image.
Hi Todd, I think you can accomplish everything without neon (except there will not be shadows). You can change the appearance of the distance monitor by opening the Pseudobond Panel (under Tools... Inspectors), clicking the line for the distance monitor, and then clicking "attributes" on the right. This will bring up an attributes panel in which you can change the color, length of dashes, etc. However, you can't get rid of the number (the distance), so another possibility is to create a pseudobond with PBReader (under Tools... Utilities), and then edit that pseudobond's attributes in the same way. PBReader just takes an input file listing the atom pairs you want lines drawn between. I attach an image with one pseudobond I made this way and one that is a distance monitor. Of course, it's not your same structure. It is pdb entry 1zik, and here is the input to PBReader I used: :27.a@nz :22.b@oe2 black The color is optional, and you can change it in the attributes. Other stuff I did was to make the background white, and in the Effects tool, turn off depth cuing and increase subdivision quality, but it seems like you have a handle on those things. Caveat: there is currently a bug that results in compressed dashed lines in the image you get after supersampling. You can try making the dashes extra long within Chimera to compensate for now. For this image, the dashes looked normal in Chimera but as you can see, they look more like hashed solid lines in the image. 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
Elaine's suggestions are all excellent. There is one further option: make the label transparent. Do this by selecting a distance (control-drag across a distance) and then use up arrow to select all distances. Bring up the Selection Inspector by clicking on the button at the lower right of the Chimera window. Make sure you are inspecting "Pseudobond" and use the color well next to "label color" to change the label color to transparent. --Eric On Mar 8, 2005, at 3:07 PM, Todd Weaver wrote:
Dear Chimera-
Wondering if there is a way to combine ball-n-stick rendered with neon and displaying distances as dashed lines with ribbons for other parts of the protein. I have attached an image captured with save, all looks good except the distances are not displayed as black lines because it has not gone through neon. If I run neon the ribbons do not show up. I would like to have both in the final image.
Warmest regards,
TOdd -- Todd M. Weaver, Ph.D. UW-La Crosse 1725 State Street Chemistry Department 4020 Cowley Hall La Crosse, WI 54601 Ph. (608)785-8269 Fax (608)785-8281
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participants (3)
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Elaine Meng -
Eric Pettersen -
Todd Weaver