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. 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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users