[chimerax-users] .chimerax and PhosphoSitePlus

[Elaine Meng]

Hi Daniel,
Actually the .chimerax file (surprisingly enough) is only for Chimera, not ChimeraX.  It is the suffix we chose long ago, before the existence of ChimeraX, to use for Chimera web data:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.html>
<https://www.rbvi.ucsf.edu/chimera/docs/webservices.html#webdatasites>

It's unfortunate that the PhosphoSite Plus website calls it a "ChimeraX script," which makes it even more confusing.

So as expected, you cannot open it in ChimeraX, but as far as I know it should have opened in Chimera.  Given your description, I can only guess that something broke between when it was implemented by the Phosphosite Plus folks and now, but I don't know specifically what's broken.

I also get the rainbow pinwheel of annoyance when trying to open the chimerax file in Chimera.  I'll make a bug ticket and let you know if we figure anything out.  I was thinking if it had worked in Chimera, then you could try Chimera's menu: File... Export Scene and use the somewhat experimental export to ChimeraX script.  That would create a python script to open in Chimera.   But we are not there yet, if the webdata file doesn't work in Chimera in the first place!

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> 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. From what I read in the documentation 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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