Today i restrted my phaser becuase an entire face on the side was missing so im sadly back to square one

daily Blog 3/27/2013

3/27/2013

Today I worked on Maya, I was able to get further on the phaser i scaled both pictures to match the model and i lined up the vertices to match it more,  I worked a little with mMaya today, I tried a new virus, it was the virus for polio.

Austin's mMaya (Molecular Maya) Day 1

I am starting a new project in mMaya using the molecules of the month from the protein database, I chose Bacteriophage phiX174. I need to do 5 renders

• CPK
• Ball-and-Stick
• Ribbon model
• Contact Surface Models
• Biological unit                       

This is my CPK:

My Ball and stick:

 My Ribbon Model:

My Contact Surface models

My Biological Units:

• Explain the purpose of each model type, a CPK, Ball & Stick, Ribbon model, a contact surface models, and a biological unit.

Each Model represents a different way of showing the same thing. Like the CPK shows each different atom  clumped together, and the ball and stick is similar besides the fact that it also shows the bonds between the atoms.  The ribbon shows the overall path and organization of the protein backbone in 3D, and serves as a visual framework on which to hang details of the full atomic structure. And the contact surface is sort of just a rough demonstration of the molecule, The biological units are what it actually is and looks like

• With the CPK and Ball-and-Stick model, what do the colors represent – specifically? 

The Table is not mine, I grabbed it off of Wikipedia

hydrogen (H)	white
	carbon (C)	black
	nitrogen (N)	dark blue
	oxygen (O)	red
	fluorine (F), chlorine (Cl)	green
	bromine (Br)	dark red
	iodine (I)	dark violet
	noble gases (He, Ne, Ar, Xe, Kr)	cyan
	phosphorus (P)	orange
	sulfur (S)	yellow
	boron (B), most transition metals	peach, salmon
	alkali metals (Li, Na, K, Rb, Cs, Fr)	violet
	alkaline earth metals (Be, Mg, Ca, Sr, Ba, Ra)	dark green
	titanium (Ti)	gray
	iron (Fe)	orange
	other elements	pink

• What is a Biological Unit and how do you know if your protein 

A biological unit is a way to demonstrate the way your molecule looks in reality  

• What is a Capsid?

 A caspid is the protein coat or shell of a virus particle, surrounding the nucleic acid or nucleoprotein core.

• Ambient Occlusion, what is the relevance to molecular visualization?

• What do you think are the advantages of molecular graphics done with Maya versus other visualization tools?

I think its more user friendly, and could just have a better visuals and be a 3d visualization program that supports modifications and toolkits/plugins.



The Other information for this molecule is:


Client Model -Choose one protein from the Molecule of the Month archive and find the following:

• Molecule 

 Bacteriophage phiX174

• PDB ID Number 

 1CD3

• Author(s)

 Dokland, T.,  Bernal, R.A.,  Burch, A.,  Pletnev, S.,  Fane, B.A.,  Rossmann, M.G.

• type:

Virus

• Number of Chains:

 1 , 2 , 3 , 4

• What is the function of this protein? 

 Since this Molecule is a virus its main purpose is to utilize cells to reproduce and send out more copies to cause harm to organisms

• Where is this protein found (type of organism and/or cell type) What is the biological relevance of this protein? 

 Its a Virus so I'd say Humans/Animals

• Are any diseases associated with this protein? If so, elaborate on how understanding the structure of the protein may be important. 

 It is a disease because it is a Virus

mmaya

mMaya

Dalily Blog 3/15/2013

Today I did a lot i worked a little bit on my phaser project

I had to rewatch parts of the video to avoid confusion I also played more with nCloths for a bit