# Visualisation

## September 5, 2022

Paper model DNA

Creating visual models can be very beneficial educationally, while you can do this using software and view in on screen, sometimes building by hand can be very beneficial, and perhaps therapeutic too. If you are studying biology then DNA plays a part in this subject, so building a model of the DNA molecule (or part of it) is useful PDB101 has a nice paper model of this, which we can look at building at a future STEM Group meeting at Paignton Library.

In the meantime you can still use Rasmol and OpenRasMol to visualise molecules and other structures.

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## August 8, 2022

Jupyter Notebook intro

If you are interested in Sciences and I think with this specifically data science or science generally then it seems that Jupyter notebook is very popular and powerful tool.

The following is an introductory video.

Jupyter Notebook Tutorial: Introduction, Setup, and Walkthrough

If there is interest, perhaps we can look in to this at a future STEM group meeting and try and invite someone along who may be able to help explain and or demonstrate further.

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## July 23, 2020

Molecular modelling with clay part 3

Further to the post earlier I am having mixed results trying to make double bonds from bendy straws. This is really proving to be not the most ideal solution.

I am experimenting with using straight straws side by side to represent a double bond.

This sort of works, but still isn't ideal, perhaps I'll just stick to single bond molecules.

Doing modelling with clay is certainly not an ideal solution but, as stated it may simply help with some basic modelling if you can't get hold of the actual modelling kits.

Just don't try and be adventurous.

This is science, so it needs some more experimentation to find an ideal solution.

if anyone has those craft match sticks such as these:-

as sold by Factory Direct Craft.com

This may prove to be a better solution than straws. You can get shorter lengths which will probably be better.

Don't go and buy any, I would suggest to see if you can get a few to experiment with, after school or other child care clubs usually have craft materials, so I would suggest experimenting first.

## July 23, 2020

Molecular modelling with clay part 2

As discussed in my post yesterday. I am going to introduce how to build a few a basic molecules with the resources suggested.

Step 1

Firstly I have cut the Black and White modelling clay to size.

The sections on the RIGHT can be put away for later use. You can see I have more White clay for Hydrogen than Black which I am using for Carbon.

Step 2

Now cut the clay up, roll in to balls and assemble the straws (links) that are needed (in this case 4) It is a good idea to make sure you have all the bits you need to hand.

The Carbon is bigger as we need to attach the 4 Hydrogen to this.

So here, is our Methane model, partly assembled. I have left the last one off for illustration.

The final step is to attach the last Hydrogen to the Carbon creating Methane $CH_4$.

Hope this helps, it may not be perfect but it may help if you can't get hold of actual Molymod kits.

Hopefully what this will allow you to do is visualise basic chemical structures.

There is an addition to this post here

## July 22, 2020

Molecular modelling with clay part 1

About a month ago, I started a discussion on the Qoto Discourse forum on molecular modelling.

As I am aware not everyone can afford the Molymod kits [1], I suggested that it should be possible to do something similar, at least on a basic level with plasticine. As I didn't have any at the time, I made a rough model using BluTack.

I have since managed to find some modelling clay from Poundland [3] so I present here, part 1 of 2 on a how_to do this.

Note: is was suggested that I make a video of this, I don't have the equipment for this, so will use photos instead, however hopefully once the South Devon Tech Jam [4] is back, perhaps I can get some help with making a video.

I would rather use photos than make a really bad video, and seek some expertise in creating a video.

So as mentioned in the Discourse thread [2], which you are welcome to join and add to the discussion. What we are looking to do is build simple molecules.

This above shows some basic Alkanes made with a Molymod kit [1].

So firstly the clay I bought from Poundland is below

I have already cut some drinking straws to length

So in this case, the straight pieces are about 1” and the bendy pieces are about 1” either side of the bend.

And as mentioned before these can act as part of a double bond or straight bonds.

As also discussed the Colours will follow normal convention:

Colour Atom
Black Carbon
Red Oxygen
White Hydrogen
Blue Nitrogen
Green Halogen

This system using the clay isn't going to be perfect, but it is not meant to be. If we can build basic molecules, this is the important thing.

I will provide a follow up post tomorrow.

References

End notes

Hopefully this is useful and if it is, I am still looking for employment in a school, I feel that being able to think of solutions such as this, demonstrates important skills such as problem solving, and writing these blog posts also demonstrates communication skills.

You can find a link to my LinkedIn profile and other contact details on my contact page here.