[Chimera-users] ksdssp assignments

Elaine Meng meng at cgl.ucsf.edu
Fri May 7 09:48:56 PDT 2010

I can only reiterate my first reply:
Sorry I don't have anything more specific to tell you,

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.

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