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Re: Modeller - Chain IDs



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