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@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@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@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
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