[Chimera-users] queries on making image
meng at cgl.ucsf.edu
Thu Nov 9 09:22:00 PST 2006
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:
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
> 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:
> 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:
> Thanks in advance,
You're welcome. I hope this helps!
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
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