Marvin Structure Renderer

Hi,

I have been having this problem for a while now across various KNIME versions, at least since KNIME 2.9.

Sometimes without reason, when viewing the table from a node output, the row heights are huge (bigger than the screen height per row) from the structure rendering. I do not know what causes this. I will manually resize the row height back to a normal height, and if I shut the window down and reopen, the row heights are massive again.

If I go to the Marvin Renderer settings, the Marvin render preferences seem to be set correctly, with row height and column width at 65 px, with Automatic Scaling on, and scale factor in units of bond length at 26.4.

If I change the row height from 65 to another value, and then back again to 65, then the row heights return to a normal height. But again at some point, they will just suddenly become really large again.

Any ideas?

Simon.

Hi Simon,

I'm sorry that I have never seen the problem in my environment...
Is it possible that you give me example flow / data?

Best,
Taka

Hi Taka,

thanks for getting in touch, unfortunately I have never found anything specific to cause it. It just suddenly happens and it occurs in every workflow I have open in Knime. Even closing Knime and restarting doesn't fix it. I have to go into the Knime marvin renderer settings and change the row and height size by 1, and then it returns back to the normal size.

i wish I could give more information. It's happened across multiple Knime versions too.

simon.

 

Hi Simon,

I have a question.
What kind of format do you use on the Marvin Renderer?
Have you had this problem with any formats that are supported by the Marvin Renderer?

Best,
Taka

Hi Taka,

Ive been using KNIME again today, and again it just went from normal sized structures to really big ones.

It seems to happen on all formats of structures, SMILES, SDF, MOL.

 

I've never had this issue with other renderers such as RDKit or Indigo.

Simon.

Hi Simon,

I'm sorry that I have a question again.

Does this problem occur to only the height direction?
Does this problem occur to all except for your PC?

Thank you for your time and kindly cooperation.

Best,
Taka

Hi Taka,

it happens to both the height and the width. It always goes to a very big width and very big height.

i wasn't sure what you meant by your second question. I have only observed this problem on my PC, I haven't seen it on the Mac, but I don't use Knime on the Mac anywhere near as much as on the PC.

simon.