[Chimera-users] Autodock Vina plugin

Ralph Loring rhloring at gmail.com
Wed Jan 5 09:56:20 PST 2022

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.
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

On Wed, Jan 5, 2022 at 12:13 PM Elaine Meng via Chimera-users <
chimera-users at cgl.ucsf.edu> wrote:

> You can remove hydrogens from the protein part only using Chimera (or
> ChimeraX) command:
> delete H & protein
> That would not include the water, however.  You could also do this to
> remove water hydrogens:
> delete H & solvent
> 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 12:50 AM, Enrico Martinez via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> > [...]
> > one question:
> > how I could remove only protein's Hydrogen atoms using Chimera's
> > command line (keeping them on the ligand)???
> >
> _______________________________________________
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