<div dir="ltr"><div>Hi Tony and Elaine,</div><div>These are very helpful suggestions and with some fiddling, I was able to get comparable results between ChimeraX and Chimera publication preset 1. However, it seems that ChimeraX is more sensitive to image size and so more fiddling may be required depending on the size of the image.</div><div>These are the settings I ended up with (but others may like different looks):</div><div>
<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif">graphics silhouettes width 2<span></span></p>
<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif">graphics silhouettes depthJump 0.007<span></span></p>
<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif">lighting depthCue false<span></span></p> The default setting for material seemed fine.</div><div>I'll try to set this up as a custom preset as you indicated.</div><div>Thanks!</div><div>Ralph<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jan 5, 2022 at 1:43 PM Anthony James Schaefer <<a href="mailto:tony.schaefer@uga.edu">tony.schaefer@uga.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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Ralph,</div>
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It looks like the Chimera 'publication 1' preset turns off depth cueing, while the ChimeraX 'publication' preset does not change depth cueing (it looks like it's turned on in these images). Depth cueing could be contributing to the washed-out look of features
that are farther from the screen. You can turn it off in ChimeraX with</div>
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lighting depthCue false</div>
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It might also have something to do with lighting intensity. I'm not sure how Chimera and ChimeraX differ in that regard.<br>
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The Chimera models also look more reflective. You can try running</div>
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material shiny</div>
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to see if that looks better. <br>
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<a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/lighting.html" id="gmail-m_-6778714259645981827LPNoLPOWALinkPreview_1" target="_blank">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/lighting.html</a><br>
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<a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/material.html" id="gmail-m_-6778714259645981827LPNoLPOWALinkPreview" target="_blank">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/material.html</a><br>
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Best,</div>
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Tony<br>
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<div id="gmail-m_-6778714259645981827divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> ChimeraX-users <<a href="mailto:chimerax-users-bounces@cgl.ucsf.edu" target="_blank">chimerax-users-bounces@cgl.ucsf.edu</a>> on behalf of Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br>
<b>Sent:</b> Wednesday, January 5, 2022 1:17 PM<br>
<b>To:</b> Ralph Loring <<a href="mailto:rhloring@gmail.com" target="_blank">rhloring@gmail.com</a>><br>
<b>Cc:</b> <a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a> <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>>; <a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a> List <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>><br>
<b>Subject:</b> [chimerax-users] pub preset: Chimera vs. ChimeraX silhouettes</font>
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<div>[EXTERNAL SENDER - PROCEED CAUTIOUSLY]<br>
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Hi Ralph,<br>
It looks like the difference between the pub presets of Chimera and ChimeraX is all in the silhouette edges (black outlines), and that what you want is for them to be thicker and drawn in more places. These are the silhouette linewidth and depthJump parameters,
which can be controlled in the ChimeraX "graphics silhouettes" command:<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes</a>><br>
<br>
E.g. to make them fatter in ChimeraX<br>
<br>
graphics silhouettes width 3<br>
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....and drawn in more places<br>
<br>
graphics silhouettes depthJump 0.01<br>
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As I understand it, the reason the preset can't make these exactly 1-to-1 between the two programs in all situations is that it depends on the graphics windowsize, the size of the image that you save, and depth (Z-range) of the data that is shown, since depth
jump is a fraction of that rather than a specific distance. So if you had a smaller protein it would be better about drawing the silhouettes around individual parts of the ribbon.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Jan 5, 2022, at 9:56 AM, Ralph Loring <<a href="mailto:rhloring@gmail.com" target="_blank">rhloring@gmail.com</a>> wrote:<br>
><br>
> Hi,<br>
> I've been trying out ChimeraX v. 1.3 vs. Chimera v. 1.15 on the same computer and notice that the publication presets for Chimera (Preset publication 1) look to my eye far superior to the preset publication setting for ChimeraX. This is really noticeable
when comparing side by side at 400% enlargement. The attached tif file was created from powerpoint at 300 dpi comparing the same set of pdbs superimposed using Matchmaker from similar vantage points (but colored differently) and saved as tiff files or copied
using screenshots. To my eye, the screenshot of the Chimera image is better than the ChimeraX tiff and the Chimera tiff is the best of all. The alpha helices in ChimeraX look washed out and the shading is less defined. Is there any way to get comparable
images to the Chimera preset publication 1 in ChimeraX?<br>
> Also, although these images are from the same pdb sources, it seems that the backbone ribbon is much more jagged in ChimeraX. Is there more smoothing in the algorithm for Chimera? Not that it matters that much, but I'd just like to know.<br>
> Thanks,<br>
> Ralph Loring<br>
> Associate Professor of Pharmacology<br>
> Department of Pharmaceutical Sciences<br>
> 166 TF<br>
> Northeastern University<br>
> 360 Huntington Avenue<br>
> Boston, MA 02115 USA<br>
> 617-373-3216 office<br>
> 617-373-8886 fax<br>
> <a href="mailto:r.loring@northeastern.edu" target="_blank">r.loring@northeastern.edu</a><br>
<br>
<br>
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