Friends, What is the best way to generate an image of fixed size. Say i want to create an image of 4,4 (width, height) at 300dpi. I tried the following windowsize 1200 1200 When i go to save image--> I saw the pixel width and height changed as *1200, 618* ( I dnt understand why this changes although i set as 1200 1200). So i set the print unit as 'inches', then i entered width and height as 4,4. The final image that it produced has different width and height (4, 6.13). Thanks, Bala
Hi Bala, It is not necessary to make the window the same pixel size as the image you want, only the same width:height ratio (aspect ratio). If you want a square image, make the window square at whatever size is convenient. Then in the File... Save Image dialog you can specify any pixels, or use inches with a dpi value. The Save Image dialog has an option "Maintain current aspect ratio" that is turned on by default. You would need to turn that off to save an image with a different aspect ratio than the window, but I don't recommend that because the window would not show what the image would contain. This tutorial includes a section on setting image size: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/images.html#saving
I don't know why windowsize did not give the size you specified -- it works in my tests. At first I thought it was because that was bigger than your display, but at least on my Mac it worked to make the window bigger than my display: windowsize 1200 1200 did give width 1200 and height 1200 in the save image dialog. Since that size is not convenient (I can't see the command line) I then entered windowsize 800 800. Next I tried image save with dimensions of inches, dpi 300, width 4. The "Maintain current aspect ratio" option was turned on, so simply clicking in the height area sets it to 4. The image saved that way did have the correct size (1200 x 1200 pixels, 4" x 4") as reported by Photoshop. If things are not working on your machine, you should use "Help... Report a Bug", describe what you did, attach any important files, and include your email address if you want a reply. That will include information about your machine, since I cannot reproduce the problems you are describing. Best, 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 Dec 11, 2009, at 3:21 AM, Bala subramanian wrote:
Friends, What is the best way to generate an image of fixed size. Say i want to create an image of 4,4 (width, height) at 300dpi. I tried the following
windowsize 1200 1200 When i go to save image--> I saw the pixel width and height changed as 1200, 618 ( I dnt understand why this changes although i set as 1200 1200). So i set the print unit as 'inches', then i entered width and height as 4,4. The final image that it produced has different width and height (4, 6.13).
Thanks, Bala
Dear Elaine I am planning to generate a couple of figures using the new coulombic surface coloring tool. Can you give me any pertinent details that I might include in the Figure legend describing how the surface is generated. thanks Kevin Dalby Dalby, Kevin N., Ph.D. Associate Professor, Southwestern Drug Corporation Centennial Fellow Med. Chem. BME 6.202B (512)471-9267 http://web.me.com/dalbykn dalby@mail.utexas.edu
Hi Kevin, If you click the Help button on the Coulombic Surface Coloring tool, it will bring up the man page with all the details in the browser window. The documentation is included with your download, but here are the corresponding pages on our Web site: Coulombic Surface Coloring: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic...
... "The calculation requires charge assignments, which in turn require hydrogens. An existing structure lacking hydrogens is not changed, but a copy is created in memory, protonated, and assigned charges, which are then transferred to the existing structure. Where hydrogens are missing from the existing structure, their charges are collapsed onto the adjacent heavy atom." ... Details of charge assignment: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge...
You will need to decide what level of detail is appropriate for your legend. It could be as little as something like "colored by Coulombic electrostatic potential in Chimera" if you've also included a color key, or include more technical details such as the name of the tool, Chimera version, dielectric value, your choice of histidine protonation states, what colors correspond to what values etc. as one would need to reproduce the figure. Best, 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 Dec 11, 2009, at 12:39 PM, Kevin Dalby wrote:
Dear Elaine I am planning to generate a couple of figures using the new coulombic surface coloring tool. Can you give me any pertinent details that I might include in the Figure legend describing how the surface is generated. thanks Kevin Dalby
participants (3)
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Bala subramanian -
Elaine Meng -
Kevin Dalby