Once you are done with modeling, make another top file like this one:
######### READ_MODEL file='LONGSEQ.pdb' RENAME_SEGMENTS SEGMENT_IDS = 'A' 'B' 'C' , RENUMBER_RESIDUES = 1 3 3 WRITE_MODEL FILE='SEGMENTED.pdb' ###########
This will take the resulting model with 1000+ residues (LONGSEQ.pdb: continuously numbered and no chain IDs), but TER records included as you defined in the alignment file by '/'.
Next, in the above top file I assumed that there are 3 segments, they will be labeled as A, B, C and each segment will be renumbered and start with the specified starting numbers, in this case with 1, 3 and 3 respectively.
So, look at the RENAME_SEGMENT command for details.
If you do not mind I am sending this reply to the list as well, since this question was not discussed so far.
> Dear Andras, > > I have a question concerning the modelling of my hexamer > with the modeller version you gave me: > > I used the hint on the mailinglist concerning modelling > hetero-trimers in 1998 - to use the slash / to identify a > new chain - it works fine, but Modeller does not insert > any chain IDs... (there are IDs in the template). > This means the aa-id-numbers increase to over 1000, and > in the PDB-format, only three numbers are allowed for one > chain, so the visualization programs cut off the first number > and start again with 000... > > How do I get the chain-IDs and a correct aa-numbering? > > Thanks, > Thorsten