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OKDMol : revolution in the making ????



This is a test blog to see if image alignment etc is fine or not in the blog. These are files generated by OKDMol, a program I am writing since I am not very happy with the available softwares for viewing PDB files. This is a work in progress, and the final version will have all the features that I have been wanting in a PDB viewer. As of now, OKDMol is dependent on POVRAY, but I plan to write my own renderer soon to make things easy for me and also discard all the extraneous stuff that POVRAY has which I will not be using. Now, on to what I have done so far.

The first one is a standard VDW view :




Fig 1. VDW view of a PDB file showing the colors used for various atoms. C (grey), N (Blue), O (Red), H (White) and S (Yellow).

I think the VDW view has more depth than images drawn in other softwares. I will work on improving it further.

Next is a VDW with a HETATM (Cu) shown exaggerated. Note the copperish appearance of the HETATM. I plan to do that for all HETATM, and make it even more cool.



Fig 2. VDW view of a PDB file showing the colors used for various atoms. C (grey), N (Blue), O (Red), H (White) and S (Yellow), with the HETATM (Cu) shown in a copper texture.


The next one is what I call a dumbbell trace model. I guess this will be useful when a reduced representation is used. I have not thought much about it. Just for fun.



Fig 3. View of a PDB file showing a funny representation of the backbone trace which I call as dumbbell trace.


Last my attempts at finding helix axis and drawing cartoon mode for PDBs. This is a work in progress as you can see from the next picture.




Fig 4. View of a PDB file showing the helix axis at each residue averaged over four residues. The cylinders are drawn according to the helix axis around the local helix axis. The smoothening of the axis and also the actual 'helix' has to be coded still. Notice the cool looking greenish textured CPK of the helix atoms.

Will keep updating about the software. Right now I am stuck with writing my stupid thesis [hence the Fig numbers on a fairly informal blog :) ]. I have wasted five years of my life on it, so there is no point leaving it without getting a degree, so I guess I have to. Anyways, I am still trying to figure out how to incorporate openGL in GTK (gtkglarea ?), so it will take some time.

Comments

Garima said…
Keep going motuuuu!!!! :)
You know then in my next paper i can say " Modeled using OKDMol" :D
And BTW ..... the comp is cool!
January 8, 2010 at 5:31:00 PM GMT+5:30
Unknown said…
I can see a nobel prize in the making, Great Saale Sahab!!!
January 11, 2010 at 12:05:00 AM GMT+5:30
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