Re: [Jmol-users] Overlapping secondary structure elements in PDB

[Rolf H. <rh...@fl...>]

Bob Hanson wrote:
> Rolf Huehne wrote:
> 
>>      Hi,
>>
>> I noticed that in the PDB file of PDB entry '1AMR' there are overlaps
>> between different secondary structure record types, e.g.:
>>
>>  HELIX   13  HM PHE A  352  LYS A  355  1
>>  TURN    16 T16 ILE A 353  GLN A 356     TYPE I
>>
>> This was quite unexpected and I searched for such overlaps in all
>> remediated PDB format files of the PDB. My script detected overlaps in
>> 2032 entries. A text file containing the PDB codes and the corresponding
>> number of overlapping residues is (temporarily) available at this URL:
>>
>> http://www.fli-leibniz.de/~rhuehne/jmol/analyze_sec_struct-2008_02_26b-overlap.txt
>>
>> (Note: The numbers are not always correct because for simplification and
>> speed-up I didn't took into account numbering irregularities in the
>> non-border residues of an element, like insertion codes or nice residue
>> number sequences like "28,328,29" in entry '1BLB'.)
>>
>> The full logfile is (temporarily) available at this URL:
>>
>> http://www.fli-leibniz.de/~rhuehne/jmol/analyze_sec_struct-2008_02_26b-log.txt
>>
>> Q: Are the Jmol developers aware of this problem?
>>
>>  
>>
> yes
> 
>> Q: How is or should this be handled by Jmol?
>>
>>  
>>
>    *
>    * We do turn first, because sometimes a group is defined
>    * twice, and this way it gets marked as helix or sheet
>    * if it is both one of those and turn.
>    *
> 

So it is handled by using this priority list (helix/sheet inferred from
example '1B7Y' where helix overrules sheet):

  helix > sheet > turn

Q: What is the reasoning behind this priority list?

Q: Shouldn't such faulty information rather be discarded?

Regards,
Rolf