Protein descriptors in knime using chemistry external tool

[hrshita]

Hi,

I’m implementing a knime workflow to calculate protein descriptors of a protein by inputing its fasta sequence. I tried using the chemistry external tool node to calculate these features as outlined in this workflow:

Protein descriptors – KNIME Community Hub

Calculates protein descriptors based on protein structure and sequence (Protein descriptors) or based on protein sequence only (Sequence Descriptors). Input(s): Protein structure in .mae file format for structure and sequence based descriptors or Protein sequence in .fasta file format for only sequence based descriptors. Output(s): - List of the calculated descriptors This is a companion discussion topic for the original entry at https://hub.knime.com/-/spaces/-/latest/~4GQ_xJ9w0jUnDf0w/

But, I don’t get any features as any output but rather an empty column saying text and it’s splitting my fasta input into name (string) and sequence(Seq). Can someone help me on what am I doing wrong here?

[ScottF]

Hi @hrshita -

Since this question is specific to the @Schroedinger extension, I moved it to the appropriate forum category. Now that I have tagged them, maybe they can jump in to provide additional assistance. (Also maybe @Alice_Krebs may know?)

[Katalin]

Hello,

Sorry to hear that you run into problem when trying to calculate the sequence based descriptors using the calc_sequence_descriptors.py script.
Can I please check with you which version of the Schrodinger suite you are using?
A quick test to check the problem further would be to run the script outside of Knime using:

$SCHRODINGER/run -FROM psp calc_sequence_descriptors.py -h

command to see if this will show the help text and you can then use this specify the input sequence and see if the calculation would work ok?

If the problem still remains, please send us the details you see in command line or from the Console view from Knime and we will be able to help you further with this.
If possible, please reach out to help@schrodinger.com directly and we will be able to help you further this way as well.

Many thanks,

Katalin