Hi Thorsten,
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.
Andras
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
--
,
Andras Fiser, PhD # phone: (212) 327 7206
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras