Well - I usually work in confunction with the graphics, so you can look
at the regions which differ.
I start with the rms difference. If that is > 2, I think there are
significant changes. So then you have to decide what Q you are asking,
and why. Is it that you want to use a model for Molecular replacement,
or gain insight into possibly different biology and so on?
Is there a loop which is very different?
Are there domains which shift relative to each other?
Is one structure more reliable than the other?
And so on..
Eleanor
On 04/04/2011 08:29 AM, Sandro Renato Dias wrote:
Dear all,
I´m doing some comparissons of main chain conformations using LSQKAB
and I would like to know from you how can I quantify a delta atom
result.
For instance, when I compare two identicals main chains I have the
following result:
0.001 1C A 1C A
0.001 2N A 2N A
0.001 2CA A 2CA A
0.001 2C A 2C A
0.001 2O A 2O A
0.000 3N A 3N A
0.000 101C A 101C A
0.000 102N A 102N A
0.000 102CA A 102CA A
0.000 102C A 102C A
0.001 102O A 102O A
0.000 103N A 103N A
But when I compare two different ones I can get something like this:
1.312 1C A 1C A
1.399 2N A 2N A
1.725 2CA A 2CA A
3.079 2C A 2C A
5.293 2O A 2O A
2.280 3N A 3N A
1.327 101C A 101C A
1.226 102N A 102N A
1.858 102CA A 102CA A
2.928 102C A 102C A
2.875 102O A 102O A
4.038 103N A 103N A
My main objective is to define how similar these conformations are.
But I don´t know how many angstroms is sufficient to affirm that the
both are identical or very closer so I can exchange each other.
Thanks for any suggestions.
Sandro
---
M.Sc. Sandro Renato Dias
PhD. Student in Bioinformatics
Laboratório de Biologia Estrutural
Instituto de Ciências Biológicas
Universidade Federal de Minas Gerais
http://lattes.cnpq.br/5300421458375793
