[Chimera-users] ksdssp assignments

Eric Pettersen pett at cgl.ucsf.edu
Mon May 10 16:42:32 PDT 2010

On May 7, 2010, at 6:27 AM, Tom Duncan wrote:

> On May 6, 2010, at 6:32 PM, Elaine Meng wrote:
>> At first I thought you meant you ran DSSP yourself.  How do you  
>> know that the secondary structure in the PDB file of 1aqt came from  
>> DSSP?  I thought that PDB structure depositors were at liberty to  
>> define secondary structure as they wished, which could be done with  
>> several different programs or even based on subjective opinions.   
>> In that case, it is not at all surprising for there to be  
>> differences, within reason.  I could be mistaken about the PDB  
>> protocol, however.
> Sorry for the lack of details. I was referring the annotated  
> sequence info for the PDB entry.
> Example that I mentioned: http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1AQT
> It shows a DSSP cartoon of secondary structure above the sequence. I  
> tried tweaking the parameters for ksdssp in Chimera (1.4) and could  
> not get the same as shown with the PDB sequence.

I can't get them to be identical either, thought they're awfully close:

The only difference I see is the tyrosine at position 35 (PDB  
numbering).  Is this what you're referring to?  Chimera has it as  
strand and the PDB does not.  Looking at the structure it looks like  
the PDB might be correct in that the tyrosine doesn't seem to form any  
backbone hydrogen bonds with the neighboring strand.  I'll have to  
look into this.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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