[Chimera-users] saving images -- wire representation at higher dpi

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 9 09:36:22 PDT 2008

Hi Ryan,
It is because there is an upper limit to how many pixels wide a "wire"  
can be drawn.  It varies from machine to machine. When there is a high  
final dpi and/or supersampling, that means the initial drawing needs  
to be quite fat to achieve the desired final appearance.   There can  
be a mismatch between the upper limit for the "dot" fatness (the  
atoms) and "wire" fatness.  You can probably see it without saving an  
image by simply setting a ridiculously high linewidth, for example  
with the command: linewidth 20
and zooming in so you can see the atoms and bonds.  Since the  
linewidth is in pixels and not in units of length, it is not constant  
relative to the scale of the molecule.

There is no way I know of to avoid the mismatch other than to reduce  
the amount of supersampling, the dpi, and/or the linewidth.  There is  
an attempt to estimate what linewidth is possible in saved images for  
your requested dpi and supersampling level - the File... Save Image  
dialog it will contain a message something like "effective maximum  
line width is 3.3333"

You may also want to try showing sticks instead of the wire  
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 9, 2008, at 8:24 AM, Ryan wrote:

> Hi,
> I am trying to save higher resolution images that contain some  
> residues with a wire width of 2.  I have noticed that when i  
> increase the dpi of the images, the saved images look different than  
> what is displayed in the viewer -- nodes appear at each atom of the  
> residues that are displayed as wires.  As i increase the dpi of the  
> saved images, the nodes become increasingly exaggerated (of a  
> thicker radius than the wire bonds).  Is this what should be  
> happening?  If so, is there a way to have both the atoms and bonds  
> save with the same radius?  Thanks a lot,

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