DNA, err… tape replication pictures

Here are the kind of pictures you can get by using the chemlambda visualizer.

UPDATE: Here the first video about it:

Continuing with the post

The first is a screenshot of the initial tape  with bits on it (the tape contains “1010” as an example):

tape_with_bits_0And here is what you get after 6 reductions done by the algorithm:

tape_with_bitsI’ll explain in a moment what I did.

First I wrote the   tape.mol file which represents the initial molecule.

Then I used  bash_main_viral_foe_bubbles.sh  which can be downloaded from the explanations/downloads page of the visualizer.

The script waits me to choose a .mol file,  which I did by writing at the prompter tape.mol.

Then I typed firefox look.html &  (use whatever browser with javascript enabled) to see the results.

UPDATE: Attention, just found out that in some versions of safari there is a problem with working with local files. I suspect, but if you know more then please tell me, that even if safari does handle the file// protocol and opens the look.html, it does not handle well the part where the look.html opens the json files file_0.json … file_10.json.

These json files are produced by the scripts, then they are turned into d3 force graphs by look.html.

So, it may happen that safari opens the file look.html, but when you click on the buttons to see the molecules in action, then safari fails to open the json files which look.html needs, so nothing happens further.

I don’t know yet any solution for this, other than “use firefox” for example. There should be an elegant one.

UPDATE 2: solved!  just download playall.tar.gz .


Now, everything (the scripts, libraries, the file look.html) are available at the said downloads page. This specific .mol file can be saved from the link provided.

I clicked on the “initial” button” and I got a whirling molecule. I let it settle a bit and then I used the click and drag to position some of the atoms in a fashion more understandable if there’s no move, in a picture.

Then I took the screenshot with a generic soft.

The same for the second picture, which shows what you get at step 6.  I combed the two replica of the tape (by click and drag) so that it is obvious that the replication went well.

Took a screenshot again.

And that’s it!

This is not yet part of the gallery of examples,  which I recommend in particular for getting other mol files.

The bit which I used (i.e. the green atoms molecule which is on the “tape” in some places) appears in the example named “the bit propagation“.



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