you are probably right, but the depositor can override the automatic secondary structure assignment by submitting his own. Perhaps this is what happened here.
I would recommend the original poster to generate them by hand by inspection of the structure plus density if possible - i.e. not trust any program...
Or, in case he wants to do it for a lot of structures and inspection of them all is not feasible, regenerate them all with the same version of his favourite program.
Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
On 3 Jul 2013, at 16:46, Robbie Joosten wrote:
> Hi Miha,
>
> I thought the PDB actually uses DSSP. Perhaps it is a different version,
> there have been some new releases recently. Anyway, there is no reason why
> you should stick to the assignment of the PDB. If another program gives
> slightly different results you can use those as long as you make sure it is
> obvious which program you used (cite the program).
> The next CCP4 release will have the official dssp (which is used to make the
> DSSP databank).
>
> Cheers,
> Robbie
>
>
>
>> -----Original Message-----
>> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
>> Pavšic, Miha
>> Sent: Wednesday, July 03, 2013 16:01
>> To: [log in to unmask]
>> Subject: [ccp4bb] PDB secondary structure assignments
>>
>> Dear CCP4BB members,
>>
>> what is the usual practice regarding secondary structure assignments when
>> preparing publication figures of protein structures and topology diagrams
>> from deposited PDB files? The deposited PDB files already contain such
>> assignments in the header section (using PROMOTIF?). Should these
>> assignments be "obeyed" or is it common to used other software/algorithms
>> (e.g., DSSP and Stride). In my case assignments using DSSP result in
> slightly
>> differ from PDB assignments in the regions of short alpha-helical
> structure
>> (corresponding to stretch of 4 aa residues).
>>
>> Thank you for your suggestions.
>>
>> Regards,
>> Miha
>>
>>
>> ******************
>> Miha Pavsic, Ph.D.
>> University of Ljubljana
>> Faculty of Chemistry and Chemical Technology Chair of Biochemistry Cesta v
>> Mestni log 88a
>> SI-1000 Ljubljana
>> Slovenia
>>
>> e-mail [log in to unmask]
>> skype mihapavsic
>> phone (lab) +386 1 2419 488
>> fax +386 1 2419 487
>> ******************
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