[Chimera-users] Saving Images

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 8 13:59:37 PDT 2012

Hi Eric,
One further idea is that you can use sticks instead of lines, although the sticks can't be dotted or dashed.  

Distance monitors, H-bonds, metal complexation lines etc. are all pseudobonds. One way to change a pseudobond into a stick is to Ctrl-click to select it, then use the Selection Inspector (open by clicking the green magnifying glass icon near bottom right of Chimera window) to change "bond style" from "wire" to "stick".  You can make the stick thinner by reducing the "radius" in that same dialog.  All this can also be done with the "setattr" command, as explained in a recent post:


On Aug 8, 2012, at 11:39 AM, Tom Goddard wrote:

> Also some older Chimera versions simply didn't fatten up the lines when using supersampling so they always came out too thin independent of the upper limit on line thickness Elaine mentions.  So if you are running an older Chimera or a daily build of any vintage you might try the latest production release 1.6.2.
>    Tom
>> Hi Eric,
>> When you save an image with supersampling, initially the image is drawn larger and then sampled down to the final requested size.  The problem is that graphics drivers have an upper bound on linewidth that can be drawn, so the line can only be so fat in the initial image, and then when it is sampled down, it is thinner.  The image dialog will report (near the bottom) the maximum attainable linewidth in the final image given the requested image dimensions and the supersampling level.
>> Decreasing the supersampling level and/or image dimensions will increase the attainable line fatness.  Generally supersampling is nice because it smooths edges (pixel stairsteps less visible), so I would first see if 2x2 supersampling ameliorates the problem before turning it off entirely.
>> For further discussion/explanation, see this previous post:
>> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-December/004642.html>
>> 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 Aug 7, 2012, at 2:09 PM, Hobbs, Merlin Eric wrote:
>>> We are having trouble saving images to look a certain way.  More specifically we are trying to make an image with the distance from a residue to a metal ion shown.  The problem arises when we save the image the 'thickness' of the distance line doesn't change on the actual saved image. So no matter what the thickness is on chimera the image will always show the distance line as being less thick.
>>> Thanks
>>> Eric
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