Superpose result anlysis....

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bioinfo
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Superpose result anlysis....

Post by bioinfo » Tue Mar 29, 2011 8:41 am

I have done protein structure superpositions for mine 8 sequences....
using superpose server :
URL: wishart.biology.ualberta.ca/SuperPose/

But i dont understand Global & Local RMSD for Heavy and All...I dont know their mean??

I also want to interpret & analyse my result...

I have to wright conclusion for this...& i have no idea...

You have any suggesions for that then pls tell me...

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JackBean
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Post by JackBean » Fri Apr 01, 2011 10:18 am

RMSD is the difference between location of particular proteins. You can either align the whole proteins and get the global RMSD or you can align only smaller part (e.g. the active site) and get local RMSD, while the rest of the proteins does not have to align at all.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

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Re: Superpose result anlysis....

Post by bioinfo » Fri Apr 01, 2011 4:45 pm

Thank u for RMSD defination...Jack...
But I still don't know RMSD for HEAVY & All mean...
Is it regarding atoms..???
I have given below results which i gained from server...
If you know then pls tell me...Have you used Superpose..???

Local RMSD

Alpha Carbons Back Bone Heavy All

RMSD 1.359 1.373 2.048 2.048

Global RMSD

Alpha Carbons Back Bone Heavy All

RMSD 1.359 1.373 2.048 2.048

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JackBean
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Post by JackBean » Fri Apr 01, 2011 7:28 pm

heavy means heavy atoms, which are added to the crystal, because they are more visible than the small carbons or nitrogens. And all means, unexpectedly, all atoms from the structure.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

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Trueweaver
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Post by Trueweaver » Sun Apr 03, 2011 7:23 am

thx for post's .....interesting

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Post by mohit » Sun May 22, 2011 9:09 am

Dear Jack, i totally disagree with your statement related to heavy atoms. Heavy atoms are not added to the crystal structures, Even carbon and nitrogen atoms are characterized as heavy atoms.

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