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@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@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