On Nov 9, 2006, at 8:32 AM, bala wrote:
Hello chimera users,
1) I hve to show two molecules in the same figure side by side. When i am displaying, i have a problem that both molecules are not coming at same plane. Is there any option to adjust this.
You can move models in the Z dimension (closer/farther) using the mouse: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html First, you'd want to make one model unmovable so that only the other one would move. Models can be made unmovable by unchecking "Active" in the Model Panel (under Favorites in the menu). You can see where the models are in the Z dimension by looking at the Side View (also under Favorites). Another approach is to first match the two structures and then only move them apart in the X and/or Y directions. Of course, if you rotate the whole view, that will again make one molecule farther back than the other if they are side by side. You can make each model rotate around its own center with the command "set independent."
2) I labelled both these molecules. The labels are coming fine in the screen. But when i create an image (i save it as tif file), some labels are getting hided below my molecular surface. Which option i should use to rectify that. For figures, I recommend 2D Labels (see #3 below) and not the usual labels that move with the structure. The labels that move with the structure are mainly good for interactive viewing.
3) How one can add text on the screen/near a particular spot on the molecule ? Use 2D Labels (Tools... Utilities... 2D Labels, or the command 2dlabels). These are arbitrary labels in the plane of the screen that will not move when the structure is moved. Thus, you need to position the molecule how you want it in the figure first, then add the 2D Labels. Manual pages:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/ 2dlabels.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html
4) Someone kindly Suggest me on best settings (i mean values) of the resolution based on your experience of making figures using chimera or which you normally use.
If it's for a paper to be published, usually the journal has instructions on the necessary resolution. Sometimes it is 300 dpi. If so, you'd measure the final size of the picture and multiply to give the number of pixels. If the column is 3 inches wide, for example, you would want an image in that column to be at least 900 pixels wide. Generally 300 dpi is pretty high resolution, 600 dpi really high resolution. For the web, I usually just go by how it looks to me, and end up with 300-1000 pixels wide depending on how large the image should be. For other settings relating to saved images, see the Image Tips and the "Images for Publication" tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ frameimages.html
Thanks in advance, Bala
You're welcome. I hope this helps! ----- 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