[chimerax-users] [Chimera-users] Autodock Vina plugin

[Ralph Loring]

Hi, I'm updating protein problems for the upcoming semester and translating
the instructions from Chimera to ChimeraX.  I can't find the Ramachandran
plot in ChimeraX.  Is there an add-in that I'm missing?  I don't see it
mentioned in the guide and can't find it in the help section.  If it's not
there, is there a reason it was dropped?  The students find it instructive.
Thanks,
Ralph


Ralph H. 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 12:56 PM 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
>
>
> 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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>
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