[Chimera-users] queries on making image

[Elaine Meng]

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 at 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




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