[Chimera-users] error in add chain ID

Eric Pettersen pett at cgl.ucsf.edu
Thu Jun 7 16:05:07 PDT 2012

On Jun 7, 2012, at 12:51 PM, Hamzeh, Rahimi wrote:

> Dear Eric
> use
> I want rename_pdb_for_chimera.py for adding chain ID to pdb file but  
> i got following erro.
> buksanbio at hamzeh:/media/6C166CAD166C7A4A/kit/zdock/apc10-apc3$  
> python rename_pdb_for_chimera.py 1 avgapc10final.pdb
>  File "rename_pdb_for_chimera.py", line 100
>    there's a chain identifier in the "TER" line... (the condition len
>    ^
> IndentationError: expected an indented block
> Please let me know about my wrong

Hi Hamzeh,
	I assume you are using the script from this old posting:


The problem is that the mail list software wrapped some lines into  
multiple lines and for the script to work those lines need to remain a  
single line.  Instead of trying to fix all those things you should  
just instead download the current version of Chimera (1.6.1) and use  
the Change Chain IDs tool (in the Structure Editing category) to  
assign chain IDs to the chains.  However, if you need to have the  
script work because you are processing many files, edit the script and  
go to line 100 (mentioned in the error message above) and join that  
and the three following lines to the preceding line (or delete the  
four lines that wrapped).  A few lines down you'll see another line  
that wrapped ("print it as is") and you need to join that one to the  
preceding line or delete it also.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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