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 [email protected] skype mihapavsic phone (lab) +386 1 2419 488 fax +386 1 2419 487 ******************
