Authors can supply the secondary structure assignments to the PDB and these trump the PDBs own determinations and will appear in the authors' entry.
Remarks 650 (Helix) and 700 (Sheet) are then included which allow the documentation of the origins of the secondary structure definitions and any useful details from the authors on the determination methods used (presumably down to the trivial ' this looked prettier to me than the DSSP ones'). For the record you can check the pdb annotation manual (http://deposit.rcsb.org/depoinfo/download/dp.pdf) that seems to indicate the secondary structure is cooked up by the in-house 'maxit' program. However there are some delightful sketch drawings (pages 92 to 93) showing how the annotators are supposed to work stuff out with a pencil-and-paper. This may explain cases where the annotators have included material in the secondary structure lines which were presumably helpful comments that should've been trimmed out For example in entry 3pcy: HELIX 1 A ALA A 52 SER A 56 1ONLY TURN OF HELIX IN MOLCULE 5 SHEET 1 I 4 GLY A 10 VAL A 15 0 SHEET 2 I 4 ILE A 1 ALA A 7 -1 N GLY A 6 O ALA A 13 SHEET 3 I 4 GLU A 25 ASN A 32 1 O LYS A 26 N ILE A 1 SHEET 4 I 4 GLY A 67 LEU A 74 -1 O GLU A 68 N ASN A 31 which is, I suppose useful, if you were looking for the 'only turn of helix in molcule'? Of course we can expect these quirks to be a thing of the past when the long promised wwPDB 'Common Deposition and Annotation Tool' is rolled out. This Common Tool is apparently now 'nearing readiness for testing by external users' (http://www.wwpdb.org/wwpdbac-pages/wwPDBAC2012_report.pdf). Hmm... Previously advertised as: 'completion is on track for 2012.' (http://www.wwpdb.org/wwpdbac-pages/wwPDBAC_2011_Report.pdf) or that 'substantial completion in 2011 is likely.' http://www.wwpdb.org/wwpdbac-pages/wwpdbac-2010-report.pdf or perhaps more pertinently: 'In early 2010, the annotation module will be put into service,' (http://www.wwpdb.org/wwpdbac-pages/wwpdbac-2010-report.pdf) Perhaps as in many things it is often better to travel hopefully than to arrive... Cheers Martyn Martyn Symmons Cambridge UK ________________________________ From: Mark J van Raaij <mjvanra...@cnb.csic.es> To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 3 July 2013, 16:00 Subject: Re: [ccp4bb] PDB secondary structure assignments 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >> Pavšic, Miha >> Sent: Wednesday, July 03, 2013 16:01 >> To: CCP4BB@JISCMAIL.AC.UK >> 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 miha.pav...@fkkt.uni-lj.si >> skype mihapavsic >> phone (lab) +386 1 2419 488 >> fax +386 1 2419 487 >> ******************
