<div dir="ltr"><div>Hi,</div><div>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?</div><div>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.</div><div>Thanks,<br clear="all"></div><div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div>Ralph Loring<br>Associate Professor of Pharmacology<br>Department of Pharmaceutical Sciences<br>166 TF</div>
<div>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></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jan 5, 2022 at 12:13 PM Elaine Meng via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.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">You can remove hydrogens from the protein part only using Chimera (or ChimeraX) command:<br>
<br>
delete H & protein<br>
<br>
That would not include the water, however. You could also do this to remove water hydrogens:<br>
<br>
delete H & solvent<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>
<br>
> On Jan 5, 2022, at 12:50 AM, Enrico Martinez via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br>
> [...]<br>
> one question:<br>
> how I could remove only protein's Hydrogen atoms using Chimera's<br>
> command line (keeping them on the ligand)???<br>
> <br>
<br>
<br>
_______________________________________________<br>
Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br>
Manage subscription: <a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" rel="noreferrer" target="_blank">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
</blockquote></div>