[chimerax-users] .chimerax and PhosphoSitePlus

[Eric Pettersen]

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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