RE: [modeller_usage] use NMR as template

["Luis Rosales" <ludwig AT biomedicas.unam.mx>]

Hi Remo!!

Welcome to the list, as far as I know:

- Yes you can use a NMR file, but I understand that modeller will use only
the first structure in your PDB that meets the specifications of your
Alignment file (on the 2nd line, where it says something like: 
	structureX:1fdx:1 : :54 : :ferredoxin:Peptococcus aerogenes:
2.00:-1.00  ) 

- You can use NMRClust to find how many conformationally related subfamilies
you have on your PDB, this program also finds the most representative
structure for each subfamily.

- I know this could be obvious, but Have you looked at your PDB???  Usually,
the PDB files for NMR structures tells you if there is a representative
structure for the whole ensamble and to what model correspond (Look at the
end of the "REMARK 210" ) on your PDB header. 

Hope this helps,
Good luck,

Ludwig
 

-----Mensaje original-----
De: modeller_usage-bounces AT salilab.org
[mailto:modeller_usage-bounces AT salilab.org] En nombre de remo
Enviado el: Lunes, 27 de Septiembre de 2004 11:28
Para: modeller_usage@listsrv.ucsf.edu
Asunto: [modeller_usage] use NMR as template

hi i'm Remo and i'm new with modeller...
i'd like to know if :
- is possible to use an NMR file with 24 structures as template
- how to make in any way an averaged structure and then use this one as 
template
- there are some useful tricks to handle NMR structures

i hope in your help

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