Visualizing bio-molecules in Computer[Part-2]: Introduction to Tcl scripting environment in VMD (1 SBD prize task inside) by dexterdev

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steemstem · @dexterdev · May 1 '18 (edited)

$15.02

Visualizing bio-molecules in Computer[Part-2]: Introduction to Tcl scripting environment in VMD (1 SBD prize task inside)

Hi friends! I am back with the second part of my bio-molecular visualization series. If you missed the first part, please see it here:
[Visualizing bio-molecules in Computer[Part-1]: Let us inspect a PDB file and see it using VMD](https://steemit.com/steemstem/@dexterdev/visualizing-bio-molecules-in-computer-part-1-let-us-inspect-a-pdb-file-and-see-it-using-vmd)

<center>![](https://i.imgur.com/BkR2JSE.gif)</center><sub>Simulation of a Ubiquitin molecule(PDB: 1UBQ) in water(not shown for clarity) visualized in VMD using `New cartoon` style</sub>

## Recap from the first part
- We learned about PDB file format.
- Visualized 1E6J.pdb using VMD.

---

What else can we do? When you visualize(or read it in a text editor) this PDB file in VMD, you will notice that it has multiple chains. Let us first get the information about those chains.

## Let us do more with VMD to study 1E6J.pdb


So let us load 1E6J.pdb by `vmd 1E6J.pdb` from terminal. I have changed the `perspective` view to `orthographic` from `Display` option in `VMD Main`. In the `Graphics`->`Representations`, the `Drawing Method` is chosen as `NewCartoon` and the `Coloring Method` is selected as `Chain`. We see three chains in the VMD Display. Each chain is assigned a color automatically. Let us pull this information via `Tcl` scripting language embedded in the VMD software. (I have changed the background color of the VMD from black to white for better visibility of protein chains. Let this be an exercise. I will give 1 SBD prize for the person who correctly comments first how to achieve this. :) )

![](https://i.imgur.com/A0LpQK7.png)

### Loading the Tcl scripting environment

Go to `Extensions` -> `Tk Console` in `VMD Main`. Now what you see is a window like below:

![](https://i.imgur.com/9dBmbGj.png)
Let us do these tasks:
- First, select all atoms.
- Display the total atoms in the PDB file
- Then read the chains in the PDB file and display it.

`set sel [atomselect 0 "all"]`

`set` is a command and `sel` is a variable. `atomselect` is another command which selects `all` atoms from molecule-id `0`. 

![](https://i.imgur.com/1HjQcDF.png)

All atoms in the mol-id 0 that is 1E6J.pdb are transferred to a variable called sel, which should be assigned as $sel. Let us see the number of atoms in this selection. For that give the next command:

`$sel num`

![](https://i.imgur.com/gJd0Tbh.png)

Let us try `$sel get chain` to display all chains.
![](https://i.imgur.com/FBgM7Wt.png)
Something wrong happened. It is displaying all 3 chains. But it is assigned with all atoms.H,L and P are all the 3 chains. We only want the unique list. So let us modify our code as below:
`lsort -unique [$sel get chain]`
![](https://i.imgur.com/WCx6T8Z.png)
We have displayed the name of three chains in the PDB files. Now to count the length of this list use `llength` as below:

`llength [lsort -unique [$sel get chain]]`

![](https://i.imgur.com/hej7GdM.png)

Some shortcuts for VMD in GUI-mode can be found at this link: http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node30.html

To reset the view, just press `=` key. `R` is rotate mode, `T` is translate mode. Once you press these keys while in the visualization mode, you can use your mouse to manipulate things further like to zoom-in or zoom-out using scroll button. You can use mouse right button to move the molecule is a rotation style or translation style etc after using respective keys from the keyboard once.

### Let us rotate the VMD axis

Original:
![](https://i.imgur.com/3IjzCxS.png)

`rotate z by +90`:
![](https://i.imgur.com/sdG4gOu.png)


## Coming up

- Fitting 2 similar chains
- Measuring distances between atoms
- And much more
 
## References

- Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.
- [VMD userguide](http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug.pdf)
- [VMD tutorial](http://www.ks.uiuc.edu/Training/TutorialsOverview/vmd/vmd-tutorial.pdf)
- Citing PDB related papers: See [here](https://www.rcsb.org/pages/policies#References).
- Monaco-Malbet, Stéphanie, et al. "Mutual conformational adaptations in antigen and antibody upon complex formation between an Fab and HIV-1 capsid protein p24." Structure 8.10 (2000): 1069-1077. ***(1E6J structure related paper)***

---

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---

**<center>All images without mentioning image sources are my creations or snapshots from the computer :)</center>**

## <center>Follow me @dexterdev</center>

---
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@davinci.times · Apr 30 '18

$0.51

Hi @dexterdev
We have selected your post as post of the day for our DaVinci Times. Our goal is to help the scientific community of Steemit, and even if our vote is still small we hope to grow in quickly! You will soon receive our sincere upvote! If you are interested in science follow us sto learn more about our project. <center>[![votaXdavinci.witness.jpg](https://steemitimages.com/DQmUs8VCYpQY9r1UtWtzRmBZcgfw8YCZhZZ6gyeqHAomMV5/Prova4.jpg)](https://v2.steemconnect.com/sign/account-witness-vote?witness=davinci.witness&approve=1)
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Greetings from @davinci.witness and the itaSTEM team.

👍 aboutcoolscience, rscalabrini, dexterdev

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@ied · Apr 30 '18

$0.03

wow! Never though that a graphical view of molecule could look like piece of art. Just read the first part of this too. When i saw ur article title the thing came up to my mind is a structure of orbiting electrons as like our solar system. But these bio molecules are kind of smart in the molecular universe i guess.
Jokes apart, the article is well written. Will definitely wait for the next dancing bio molecule.
Cheers.

👍 dexterdev

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@dexterdev · Apr 30 '18 (edited)

Thank you for reading these articles. It's nice to know that there are people interested in these kind of work in steemit. I was doubtful initially to start these ones in steemit. But now I have hopes.😃

👍 ied

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ied	0 B		602,048,745	100%

@ied · Apr 30 '18

$0.03

Surely its an interesting topic. I'm sure many other people haven't ever seen a dancing molecule before, as like me. So keep this up, man.

👍 dexterdev, bartelby

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@steemboy9 · May 1 '18

Amazing post! I love it. Hey UPVOTE my post: https://steemit.com/life/@cryptopaparazzi/chapter-one-let-there-be-the-man-and-there-was-a-man-let-there-be-a-woman-and-there-was-sex and FOLLOW ME and I ll do the same :)

👎 mack-bot

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