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@salilab.org [mailto:modeller_usage-bounces@salilab.org] En nombre de remo Enviado el: Lunes, 27 de Septiembre de 2004 11:28 Para: modeller_usage@salilab.org 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