When I convert mae (maestro) format to pdb , some helical part of the structure changes to loop structure. Why does this happen?
Have you used any secondary structure assignment tool like DSSP or STRIDE or just by visuaization you are telling this.
Apart from this problem, may be you can use Open Babel to convert from one file format to other and see what is happening. If not then please do send me the file
:)
Enjoy
Dear Prasun,
Yes I checked with DSSP and STRIDE , it is correct.
But when I want to visualize the pdb format (i.e., converted form mae format in maestro) in maestro, I see a changing in part of helical part at view, not coordination.
please find attach the models in two format.
Thanks
Hey I tried and its showing. Only thing I did was: Removed everything except the ATOM record. Now open in pymol and visualize it, ll show cartoon. The RMSD is also quite low........Actually PDB file format is not having anything for TURN and the helix record was also not in the PDB file format leading to the problem........:)
Hope I have answered your doubt.
You need to be careful about the definition of secondary structure in different programs as they have differing thresholds for helix geometry some are more strict than others. So a helix portion may turn into a loop region when going from one program to another. In pymol I often need to reasign secondary structure using the alter command.
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