Superpose result anlysis....

[bioinfo]

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...

[JackBean]

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.

[bioinfo]

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

[JackBean]

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.

[Trueweaver]

thx for post's .....interesting

[mohit]

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.