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