[modeller_usage]molecular modelling with multiple chains

["典范" <>]

Hello all,
Could you please tell me how to perform molecular modelling with multiple chains?   I get trouble in preparing the alignment file in this case.


The sequence of the template is as follows:

********************************************************************************
TEMPLATE:A|PDBID|CHAIN|SEQUENCE
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTD
SEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVTMMTSK
TEMPLATE:B|PDBID|CHAIN|SEQUENCE
KRRWKKNFIAVSAANRFKKISSSGAL
********************************************************************************
the residue number of Chanin A:148; Chain B:26



The sequence of the target is as listed:

********************************************************************************
TARGET:A|PDBID|CHAIN|SEQUENCE
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELADMINEVDADGNGTIDFPEFLTMMARKMKDTD
SEEKIREAFRVFDKDGNGFISAKELRHVMTNLGEKLKDEEVDEMIREADIDGDGQVNYEEFVTMMTSK
TARGET:B|PDBID|CHAIN|SEQUENCE
KLRWLKNFIAVSKKNRFLKISSSGAL
********************************************************************************
Both the two chains have the same number of residues compared with Template.


I want to model the protein-peptide COMPLEX (NOT one by one) of TARGET:A-TARGET:B taking the TEPLATE as template structure. Could anyone please help me to know how to prepare the allignment file and paste it to me?


Best regards, 
  
DianFan Li
China
2006-03-01


ps: the typical ali file in example of MODELLER 7v7 is:

***************************************************************************
P1;5fd1 structureX:5fd1:1    : :106  : :ferredoxin:Azotobacter vinelandii: 1.90:
0.19
AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA
EVWPNITEKKDPLPDAEDWDGVKGKLQHLER*
P1;1fdx sequence:1fdx:1    : :54   : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00
AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED-----------------
-------------------------------*
****************************************************************************