Appreciating the dimensions of a PDB File

A pdb file contains the x, y & z Cartesian coordinates of all the atoms constituting the protein molecule. Thus when rendered by visualization softwares like the RasMol, SPDBV or the Jmol, we are able to rotate it around various axes, visualize it in different colours, surfaces etc.

Most of us have come across 3D movies, like the recently released Ice Age 3D, which give a very real depth to image and videos as if they are not ON some screen but rather hanging in the air, thus truly making them 3 dimensional. This was achieved, in olden times, by using the green and red filters on spatially apart cameras and merging them via colored goggles. Now a days more sophisticated techniques of polarized light using polar filters is used which gives better resolution.

Here I am giving a method which enables a user to achieve that kind of depth without any fancy goggles or image, in fact I'll be using a normal PDB file and SPDBV as visualizing tool, you can use whichever tool you like.

Please follow the steps:

1) Obtain any suitable PDB file:
For this, Google the RCSB site, in the search bar type your favorite protein name, I am using myoglobin (though it is not my favorite). U can get the myoglobin pdb file here.

2) Open this pdb file in any suitable viewer, I am using SPDBV.
In SPDBV you will get 'Stereo' view in the 'Display' tab in the menu bar at the top or else press Ctrl + T to toggle stereo view.
Important note: The viewer MUST have the option of displaying in Stereo view.

3) Display this file in the Ribbon view.
For this go to 'Window' tab in menu bar and select on 'Control Panel' or else press Alt + , . Now right click on any of the "v"s in the 'show' & 'side' columns and right click in the empty 'ribn' column. This will replace the early model by a ribbon model.

4) Colour the ribbon structure suitably.
For this go to the 'Colour' tab in menu bar, go to 'act on.... ->' and select 'Ribbon'. Now again go to 'Color' tab in menu bar and select 'Secondary Structure Succession'.

Note: If your structure is in mesh form then you can 'Render in Solid 3D' by going to the 'Display' tab.

Now you should be looking at something which looks like the screen-capture below:



Here comes the hard part:

What I want you to achieve is a third image, in sharp focus, which has popped out of the screen and is hanging in the air about half way between your eyes and the monitor.

For this:

Sit about 1&1/2 to 2 feet from the monitor screen. Concentrate on the monitor screen, and move your eyeballs towards each other by trying to look at the point in between your eyes.

When you do this the 2 images on the screen merge to form a third image, stop!! and try to focus on the third image (if you keep going the three images will further separate into 4 image!!)

Now, first thing is getting the third image in between the 2 original image.
Second thing is focusing on this third image. For this move the protein molecule, a moving third image will help you get a sharp focus on it.

Once you have got the middle image into focus, you can see that it has become absolutely 3 dimensional and now no longer sits on the monitor but has popped out and is hanging in the air. Rotating the molecule you can actually see that the alpha helices are on top or behind those in the front.

Have Fun!!!

Why does this happen??

Well the effect is the simple stereoscopic effect which is more commonly encountered in sounds. Often when we are listening to MP3s using ear phones, sounds seem to travel from one ear into another essentially meaning the source is moving.

In case of vision also it works in a similar way. We have two eyes separated by some distance. Whenever we focus on an image, we actually see 2 different images by each of the eyes, these are super imposed on top of each other by our brain to form the one clear image. We also perceive depth because of this.

When we view the PDB file in stereo in the visualizer, it shows two seemingly identical images, but look closer, they are actually slightly different.
When you merge the two images and try to focus, the brain does the rest of the work and renders the image 3 dimensional.

Swine Flu ONLY infects Swine!!!

Life is going on, as it so normally does, as it is supposed to, it is so silly when we say life is going on, after all if it had stopped we wouldn't be saying anything. YET it makes the world of sense to me - that life is going on.

Meanwhile Swine Flu is going strong in Pune. Initially it was only in Pune. Then the nearby Symbiosis closed for a week. Then a girl died. The media went over board. People flocked to medical shops for buying surgical masks. Swine Flu came ever nearer all the time. All of a sudden everywhere people were walking masked. 4 girls from the girls hostel went to get themselves tested and even before the tests were done they were Swine Flu patients. Then 3 boys from the guys hostel were supposedly down with the Swine Flu. Huge posters were put up at the Univ gate which warned people about the Flu. But the Flu came ever nearer. Now a friend of a friend is down with the Flu, then it will be my friends down with the flu and then it will be me. I am pretty sure of that. But so what, every year this happens with other Flus and other viruses and other diseases.

Media of this country is the most irresponsible of all institutions. Seriously the most idiotic of all. It sucks so big f$#*ing time that I am falling short of expressing my disdain and disgust at the media. They advise all who have Flu like symptoms to get themselves tested. They do not advise that people with SWINE FLU LIKE SYMPTOM ONLY go and get themselves tested.

As a result 3000 people turn up at Naidu hospital. People sneeze, they cough, they touch and convert a thousand square feet of area into fomites with their dirty hands. The H1N1 floats every where, it mixes in warm bodies harboring other viruses, improves its own offense and defense, many of these warm bodies would grow cold as a result. More people get infected there than were before. Thats how the virus spreads. The media never gives clearly what are the exact symptoms, how to differentiate between a normal Flu and a Swine Flu, and different sources cite different experts and say different things.

And YET surgical masks are sold at signals for 5 a piece (Half to Quarter of the Price u get in Medicals). Most probably used and not disposed off properly. And YET people in crowded buses and trains cough and sneeze at other peoples' faces with gay abandon. The other person doesn't seem to mind as such anyways.

And some die, but YET some live, and thus STILL life goes on, as it is supposed to. And thats why it makes so much sense.

Donating Blood

The other day some of my friends had gone to our usual coffee hangout when they saw a Blood Donation Van there. All of them donated blood and came back proud with their certificates and Donor ID cards. So the rest of us too decided to go ahead and donate blood the next time that van turned up.

I have never donated blood in my life, even though I am O+ve (Universal Donor), a healthy individual and almost 4 kilos overweight. And it hasn't been because I do not want to donate blood or because I am scared or anything. Its simply because I have never had an opportunity to donate blood and I never took the pains to create one by going to a hospital and doing the needful. So I was pretty much determined that this time come what may I am donating blood. Well anyways we had taken the phone number of the guy who managed the van, and the next time it came, we knew it one day prior and thus I was mentally prepared to give my blood.

However when the time came to actually enter the van and get hooked to the bag, my resolve totally faltered and eventually I couldn't do it. I don't exactly don't know why.

But mostly it is because I do not trust the system. In a country where people are inherently unsanitary, where biohazardous waste lies in heaps outside hospitals, where people lack even the basic civic sense, how can I go and agree that some one without even wearing gloves, poke a needle into me and draw my blood.

The van was pretty well equipped, no doubt about that, but the guy doing the tests which are conducted before donation, was doing them near the open door without any gloves. Two girls in lab coats were just sitting there without doing anything. How do I know that the needle is indeed sterile?

Donating your own blood is an extremely noble thing to do. Whether it saves someones life or not is immaterial. And even though we never know who receives our blood, I feel it is one of the most personal of all transactions.

I know people will say that even in a big hospital, there is no way of knowing for sure if the needle is sterile or not, that the doctor wearing the gloves would have worn them since morning handling loads of patients in between. That one can go to donate blood and very easily become unsuitable to be a donor for ever thereafter.

You might say this is a figment of my imagination, well I ask what if it is not. And if there is even the smallest possibility that this is not my imagination at work, then, well I do not need to donate my blood to anybody. After all I have my whole life ahead of me.