Issue with new protein paint

[Mija Blattner]

Dear all,

I am struggling with adding my own SNVs since there has been an update.

Therefore I have two questions:

1) Is there no more the option to upload a text file with all my mutations as i did it before

2) I am not able to show the mutation without using ">". Is this normal? Eg. when I use: R158H instead if 158R>H the tool does not show the mutation.

Any idea why?

Also, you were used to have a document showing examples how the input format should look like. Can you do the same for the newest update? I use this tool a lot and I am a bit lost since the update.

Thank you, Mija

[ProteinPaint Team]

Hi Mija, 

We were not able to recreate the issue with the mutation. From both https://proteinpaint.stjude.org/ and https://proteinpaint.stjude.org/?gene=TP53&genome=hg19, using 158RH,7578457,M,X and 158R>H,7578457,M,X we created this view: 

Would you kindly share more about how this issue occurred for you, including which url you are using?

There are instructions for the new formats in the '+' button, underneath the Submit button. Please find the format you'd like to use and click on the Show details link. The instruction will appear in the same window. We also made our documentation easier to find from the github wiki, here: https://github.com/stjude/proteinpaint/wiki. 

Lastly, the option to upload file from the UI has been removed. The easier way to use your file is to create a link with a URL parameter. The documentation for how to create those links is here: https://github.com/stjude/proteinpaint/wiki/URL-parameters. 

Take care, 

ProteinPaint Team