External forces inconsistent with Create from base pairs

[RodenLuo]

Hi,

I used tacoxDNA/src/cadnano_oxDNA.py 7_icosahedron.json he -o to generate a 7_icosahedron.json.oxview file (attached below). Drag and drop it into oxview, and then Dynamics -> Forces -> Create from base pairs, the window shows the correct base pairs. However, if I File -> Save -> External forces, I get totally different base pairs. Could you please take a look?

7_icosahedron.json.oxview

[zoombya]

Hi Roden, my best guess for your problem is that you changed smth in the scene,
like nicking or ligating. This changes the strand length and we need to generate all indices new
because of that. This is done in oxview when you do the export to oxDNA configurations.
I just tried to load the example icosahedron and reproduce the issue and for me the indices are the same.
Could you please try again ?

[RodenLuo]

Hi Michael, Thanks! I tried just now on both Win10 and Mac chrome. The problem still exists. I did not do anything after drag and drop the .oxview file I attached in the original post before the screenshot. The base pairs info is already in the oxview file (generated by the tacoxdna converter), so I did not even use any findBasePairs func.

[RodenLuo]

If I load oxdna-viewer/tree/master/examples/icosahedron, and then do the following, it is indeed consistent. I didn't choose this way in the first place because this method has given me none-complete base pairs in a few cases before.

Is what shown in the screenshot the "findBasePairs" you mentioned in the other thread?