[Chimera-users] Problem with HEADER keyword in PDBs

Eric Pettersen pett at cgl.ucsf.edu
Tue Jan 14 11:25:24 PST 2014


On Jan 13, 2014, at 5:18 PM, Thomas Hrabe wrote:

> Hi everyone,
> 
> I believe I found a problem with the >HEADER< keyword in PDB files.
> Some programs may create pdbs with the header keyword specifying the origin or a name of a chain or other metadata with the coordinates below.
> PyMol understands this keyword and colors chains that have identical chain ID (see example attached) in multiple colors while chimera interprets all as one chain.

Yeah, Chimera basically ignores the (non-standard) second and third HEADER records.  As Elaine said, Chimera knows they are different chains (which you can see by showing their sequences) but you are going to have trouble using commands in some cases because there are two :110.a for instance.  You probably want the chains in different models for this reason.  You can do that either by typing "split" in the command line, or by editing your PDB file and changing the two TER records to END records.

--Eric






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