[chimerax-users] pub preset: Chimera vs. ChimeraX silhouettes

Wed Jan 5 18:43:47 PST 2022

Awesome, thanks!

On Wed, Jan 5, 2022 at 6:52 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> After some internal discussion, we've split the publication preset into
> two in order to cover more use cases:
>
> publication 1 (silhouettes)
> publication 2 (depth-cued)
>
> A shortcut you may not know about is that you can refer to a preset by any
> unique text in its name, so both "preset 1" and "preset sil" would run the
> first preset.  These presets will be in tomorrow's daily build.  They don't
> adjust silhouette (or depth-cue) parameters, just whether they are off or
> on.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Jan 5, 2022, at 12:02 PM, Ralph Loring via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Hi Tony and Elaine,
> 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.
> These are the settings I ended up with (but others may like different
> looks):
>
> graphics silhouettes width 2
>
> graphics silhouettes depthJump 0.007
>
> lighting depthCue false
>  The default setting for material seemed fine.
> I'll try to set this up as a custom preset as you indicated.
> Thanks!
> Ralph
>
> On Wed, Jan 5, 2022 at 1:43 PM Anthony James Schaefer <
> tony.schaefer at uga.edu> wrote:
>
>> Ralph,
>>
>> 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
>>
>> lighting depthCue false
>>
>> It might also have something to do with lighting intensity. I'm not sure
>> how Chimera and ChimeraX differ in that regard.
>>
>> The Chimera models also look more reflective. You can try running
>>
>> material shiny
>>
>> to see if that looks better.
>>
>> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/lighting.html
>>
>> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/material.html
>>
>>
>> Best,
>>
>> Tony
>> ------------------------------
>> *From:* ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf
>> of Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
>> *Sent:* Wednesday, January 5, 2022 1:17 PM
>> *To:* Ralph Loring <rhloring at gmail.com>
>> *Cc:* chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>;
>> chimera-users at cgl.ucsf.edu List <chimera-users at cgl.ucsf.edu>
>> *Subject:* [chimerax-users] pub preset: Chimera vs. ChimeraX silhouettes
>>
>> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>>
>>
>> Hi Ralph,
>> 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:
>> <
>> https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
>> >
>>
>> E.g. to make them fatter in ChimeraX
>>
>> graphics silhouettes width 3
>>
>> ....and drawn in more places
>>
>> graphics silhouettes depthJump 0.01
>>
>> 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.
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>> > On Jan 5, 2022, at 9:56 AM, Ralph Loring <rhloring at gmail.com> wrote:
>> >
>> > Hi,
>> > 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?
>> > 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.
>> > Thanks,
>> > Ralph Loring
>> > Associate Professor of Pharmacology
>> > Department of Pharmaceutical Sciences
>> > 166 TF
>> > Northeastern University
>> > 360 Huntington Avenue
>> > Boston, MA 02115 USA
>> > 617-373-3216 office
>> > 617-373-8886 fax
>> > r.loring at northeastern.edu
>>
>>
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