New graphic feature in update V5.32

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Chu

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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

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Message 29349 - Posted: 14 Oct 2006, 19:39:38 UTC - in response to Message 29144.  

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

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Message 29399 - Posted: 15 Oct 2006, 17:26:33 UTC - in response to Message 29144.  

Very cool!
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hugothehermit

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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.

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Profile Charlie Abrams

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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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Profile Charlie Abrams

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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

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Message 30409 - Posted: 1 Nov 2006, 4:13:33 UTC - in response to Message 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

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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
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Chu

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Message 31078 - Posted: 13 Nov 2006, 19:17:41 UTC - in response to Message 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.


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Chu

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Message 31093 - Posted: 13 Nov 2006, 23:17:14 UTC - in response to Message 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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