[chimerax-users] .chimerax and PhosphoSitePlus

[Daniel Gurnon]

Thanks for the quick feedback Eric and Elaine.

I only stumbled upon this this morning while thinking how nice it would be
to be able to highlight all post-translational modification sites in a
protein, to compare with variants of uncertain significance....I did a
google search to see if something like that already existed, and at first
glance this PSP script seemed to be the answer. But now it seems like it
would be easier to write my own script.

____________________________

Daniel Gurnon, Ph. D.
Associate Professor of Chemistry and Biochemistry
DePauw University
Greencastle, IN 46135


On Tue, Feb 23, 2021 at 1:55 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Daniel,
> The script will actually execute if you wait several minutes.  The problem
> is that in the middle of the script it adds a surface and then executes
> many, many color commands, which causes the surface to be updated each
> time.  If you move the surface commands to the end of the script, it takes
> only several seconds to execute.  It doesn't look a lot like the image on
> the web page because for some reason the script labels every residue in the
> structure.  I have attached a script with the surface commands moved to the
> end.  You may or may not want to edit the script to remove the label
> commands.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Feb 23, 2021, at 9:06 AM, Daniel Gurnon <danielgurnon at depauw.edu>
> wrote:
>
> Hi all,
> I'm interested in visualizing post translational modified positions in
> Chimera or ChimeraX, using the script generated by PhosphoSitePlus (PSP).
> I'm not able to get it working though, so I hope you can help:
>
> Here's an example of a page with an available Chimera script.
> <https://www.phosphosite.org/proteinAction.action?id=4103&showAllSites=true>
> From what I read in the documentation
> <https://www.rbvi.ucsf.edu/chimera/1.10/docs/webservices.html> about web
> services, I should be able to click the script, and it will open in a
> locally running instance of Chimera. However, in Chrome, my only option is
> to download the script.
>
> When I download and then try to open the script in ChimeraX (v 1.1), it
> tells me the ".chimerax" file type is not recognized. When I try to open it
> in the original Chimera (v1.15), I get the infinite spinning wheel of
> rainbows. These things occur whether or not I have the reference PDB
> structure loaded. Just to see what would happen, I also tried pasting the
> first command from the .chimerax file (*setattr a label Ser-89 :88.A at OG*)
> into Chimera and ChimeraX. The command executed successfully in Chimera,
> but in ChimeraX, I get the error
>
> setattr a label Ser-89 :88.A at OG
> Expected a keyword
>
> Thanks in advance for the assistance,
> Dan
> ____________________________
>
> Daniel Gurnon, Ph. D.
> Associate Professor of Chemistry and Biochemistry
> DePauw University
> Greencastle, IN 46135
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