Rosetta@home

New graphic feature in update V5.32

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Message boards : Rosetta@home Science : New graphic feature in update V5.32

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Chu

Joined: Feb 23 06
Posts: 120
ID: 61076
Credit: 112,439
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Message 29144 - Posted 11 Oct 2006 1:27:42 UTC

In the udpate 5.32, two major new features are added to Rosetta@Home graphics.

1. During Rosetta full-atom refinement stage, sidechains are shown in addition to the protein backbone to give uses a better view of how Rosetta simulation is performed. Currently, sidechains are only shown in the "Searching" box and the label "Searching_Fullatom" indicates that Rosetta simulation is in full-atom stage with all the atoms represented and simulated.

2. Users are now able to rotate and enlarge models in all the four boxes shown in the graphics. Please note that sometimes the graphic has to be enlarged to full screen in order to have models rotated in the "low" and "native" box.

Any feedbacks on how you feel about these features are appreciated. Enjoy the new look of Rosetta@Home!
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darknightcl

Joined: Sep 25 05
Posts: 2
ID: 1030
Credit: 104,523
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Message 29349 - Posted 14 Oct 2006 19:39:38 UTC - in response to Message ID 29144.

I think one word can adequately describe what I think of the improved graphics - SWEET!
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Michael G.R.

Joined: Nov 11 05
Posts: 263
ID: 11128
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Message 29399 - Posted 15 Oct 2006 17:26:33 UTC - in response to Message ID 29144.

Very cool!

hugothehermit

Joined: Sep 26 05
Posts: 238
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Message 30362 - Posted 31 Oct 2006 9:12:45 UTC
Last modified: 31 Oct 2006 9:15:13 UTC

G'day Chu,

Could you define the side chain shapes (in the graphics) for me?

I'm guessing here, but I assuming that it's the side chains that are hydrophobic/hydrophilic and I would like to know, which of these shapes (in the graphics) are hydrophobic and which are hydrophilic, ie. what should be on the inside and what should be on the outside of the protein.

Charlie Abrams Profile

Joined: Jul 25 06
Posts: 13
ID: 101683
Credit: 6,870,894
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Message 30373 - Posted 31 Oct 2006 15:55:43 UTC

Would it be possible in the next version to color the side chains according to polarity? For example, D,E=red; K,R=blue; C=yellow; A,I,L,M,F,P,W,V=green; and G,S,T,N,Q,Y,H=orange?

Maybe this is too many colors, but I know it would be fun to watch.
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Charlie Abrams Profile

Joined: Jul 25 06
Posts: 13
ID: 101683
Credit: 6,870,894
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Message 30379 - Posted 31 Oct 2006 17:09:59 UTC

Hugothehermit,

Perhaps I can give it a try:

Phenylalanine (nonpolar) = hexagon
Tryptophan (nonpolar) = hexagon and pentagon sharing one side
Lysine (polar, charged) = long zig-zag
Tyrosine (polar, uncharged) = hexagon with a stick attached
Histidine (polar, charged) = pentagon

Most of the others are impossible to distinguish unless colors are used to represent the individual atoms. If you are able to find even the ones above, you're doing really well.
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argsanu

Joined: Oct 19 06
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ID: 121907
Credit: 22
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Message 30409 - Posted 1 Nov 2006 4:13:33 UTC - in response to Message ID 30379.

Here you must be noted that what kind of discovery you have made... Please post me ...



[qu

]Hugothehermit,

Perhaps I can give it a try:

Phenylalanine (nonpolar) = hexagon
Tryptophan (nonpolar) = hexagon and pentagon sharing one side
Lysine (polar, charged) = long zig-zag
Tyrosine (polar, uncharged) = hexagon with a stick attached
Histidine (polar, charged) = pentagon

Most of the others are impossible to distinguish unless colors are used to represent the individual atoms. If you are able to find even the ones above, you're doing really well.[/quote]

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hugothehermit

Joined: Sep 26 05
Posts: 238
ID: 1310
Credit: 314,893
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Message 30414 - Posted 1 Nov 2006 5:45:52 UTC
Last modified: 1 Nov 2006 5:57:10 UTC

Thanks Charlie,
I would assume from your post (and looking at your profile) that these are standard shapes in the chemistry world, would you be able to point me to a site that has this information on it? Ideally, a chemistry for dummies type thing, as I'm unsure what the differance charge makes in polar molecules dealing with water etc...

Argsanu,
Can someone from your team, the DPC translate that, it didn't quite make sense (to me anyway)?
Mi supozas vin ne legas esperanto :?

Edit: For a bit more clarity

Chu

Joined: Feb 23 06
Posts: 120
ID: 61076
Credit: 112,439
RAC: 0
Message 31078 - Posted 13 Nov 2006 19:17:41 UTC - in response to Message ID 30373.
Last modified: 13 Nov 2006 19:18:06 UTC

That is a very good suggestion and we will think of that. Rosetta screensaver is still at the premature stage and the current set up for the graphic thread makes it difficult to import external protein graphic drawing packages. I guess if we get an graphic professional working on this, the screensaver will be more fun to watch. That is being discussed as David Baker is planning to extend Rosetta to be more interactive to end users.here

Would it be possible in the next version to color the side chains according to polarity? For example, D,E=red; K,R=blue; C=yellow; A,I,L,M,F,P,W,V=green; and G,S,T,N,Q,Y,H=orange?

Maybe this is too many colors, but I know it would be fun to watch.


____________

Chu

Joined: Feb 23 06
Posts: 120
ID: 61076
Credit: 112,439
RAC: 0
Message 31093 - Posted 13 Nov 2006 23:17:14 UTC - in response to Message ID 30362.
Last modified: 13 Nov 2006 23:31:18 UTC

Hi, I did the google search and found one nice images which may give all the information you ask for about 20 natural amino acids and their sidechains. Normally, hydrophilic sidechains tend to appear on the protein surface and hydrophobic sidechains tend to compose the protein core. However, if two hydrophilic sidechains, for example, a positively charged lysine and a negatively charged aspartate can form a very good 'compensating' interaction, they can exist inside a prtein core and they may even play a very critical role to the stability and function of the protein..

In this picture below, each bond between two protein atoms are drawn as 'stick' and so the "nodes" are atoms. Oxygen atoms are colored in red and nitrogen atoms are colored in light blue.
.
http://www.imb-jena.de/IMAGE/aa/amino_acids.gif

G'day Chu,

Could you define the side chain shapes (in the graphics) for me?

I'm guessing here, but I assuming that it's the side chains that are hydrophobic/hydrophilic and I would like to know, which of these shapes (in the graphics) are hydrophobic and which are hydrophilic, ie. what should be on the inside and what should be on the outside of the protein.



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Message boards : Rosetta@home Science : New graphic feature in update V5.32


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