Is there a method of translating DSSP output in mmcif format to the 8 class secondary structure from normal dssp output format?
I have .mmcif files where DSSP only functions when outputting in mmcif format (I cannot obtain a .dssp file). I need to translate the results into 8 class secondary structure format. Therefore I need a way to get from values of '_struct_conf.conf_type_id' to the normal 'H B E G I T S -' output.
The possible values of the conf_type_id are here: http://mmcif-beta.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_struct_conf_type.id.html
Any pointers would be greatly appreciated.
1 answer
I have found this manual: https://github.com/PDB-REDO/dssp/blob/trunk/doc/mkdssp.pdf
It gives a table mapping them, with the exception of Strands and Beta Bridges being the same symbol in mmcif format 'STRN'.
There's also a stackexchange going into detail on the differences in strands and beta bridges in DSSP: https://biology.stackexchange.com/questions/43639/what-is-an-isolated-beta-bridge
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