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 >> ******************
