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@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: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2005-October/000476.html 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 Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu