PDB Cells are not rendered properly

Hi Team,

Some of the PDB cells are garbled when it is rendered in the node’s output table. We are using PbdCellFactory.create().

What I noticed is, as the size of the cell increases, the distortion is more. 1ett is rendered properly but not the other 2.

1ett - 332 K
6i49 - 756 K
7rf3 - 8.5 M

Is this a known issue?


Hi @ravikiran ,

good question! I haven’t seen this before.

Did you use the node below where this happens?


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I have experienced similar issue with other data types: JSON or XML. It only happens when the cell contains a lot of data. As far as I understand this might be happening here as well.
I can see that @ravikiran uses Linux, so do I. Maybe it is a platform related issue.

In case it might be helpful, here is my config:

  • Kubuntu 20.04;
  • KDE Plasma 5.18.8;
  • Kernel 5.4.0-132-generic.

Hi @Artem
thanks for commenting on this! I will research this internally and come back to the thread as soon as I have a (hopefully) useful explanation.

Hi Martyna,

Yes ‘Get PDB’ is the node I am using.


It only happens when the cell contains a lot of data.

Yes exactly. See my initial query where the distortion is more with size.

Thanks. Also, is that possible to add another renderer for PDB cells which just display the title/header alone? Generally the pdbs are huge in size.

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Hello @Martyna

Just in case I took this example. I used GET Request node and simply requested https://www.instagram.com/

This is what I got:

So it’s not only the file size but more the cell size that makes the issues? as you are having only one row here.

No, it also happens when I have multiple rows in the table. Re-scaling the cell size does not help.

Hi, I can confirm we were able to reproduce this. I have created a ticket.

@ravikiran do you know of a renderer that would show less?
Would it be possible to turn this into a string and do a workaround that would filter only the top-level information? I didn’t try myself, just thinking of different ways.

Best regards,

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Dear Martyna,

do you know of a renderer that would show less?

The solution I can think of is to create a dedicated renderer (say ‘PDB Summary’) and show only the HEADER and TITLE sections. We can create a dedicated renderer from our side but since this is a general issue faced by everyone, it would be nice if KNIME can add the additional renderer and makes it default in Preferences.


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