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Dear Xiang-Jun,
1) I would appreciate a --silent option since I am running your programs on a large number of files.
2) with snap, I would appreciate a count of the files that are written out by your program and something like a zero output file message if they are no proteins processed. This would be helpful for parsing (I know that there is a screen message, but writing it in the output file should be interesting).
Thanks for considering this if you have time.
Best,
Pascal
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Hi Pascal,
1) I would appreciate a --silent option since I am running your programs on a large number of files.
Try to run the program with --silent to see what you get. In any event, you can use file redirection (http://en.wikipedia.org/wiki/Redirection_(computing)) to achieve your goal. For example,
x3dna-dssr -i=1ehz.pdb -o=1ehz.out 2> msg
2) with snap, I would appreciate a count of the files that are written out by your program and something like a zero output file message if they are no proteins processed. This would be helpful for parsing (I know that there is a screen message, but writing it in the output file should be interesting).
See reply above.
Xiang-Jun
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Hi Xiang-Jun,
I will use --silent, thanks for this. May be this option could be mentioned in the help file (-h).
Fot the second point:
in dssr, you have
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List of 12 additional files
1 dssr-stems.pdb -- MODEL/ENDMDL delineated stems
2 dssr-helices.pdb -- MODEL/ENDMDL delineated helices (pseudo/coaxial)
3 dssr-pairs.pdb -- MODEL/ENDMDL delineated base pairs
4 dssr-multiplets.pdb -- MODEL/ENDMDL delineated multiplets
5 dssr-hairpins.pdb -- MODEL/ENDMDL delineated hairpin loops
6 dssr-4pas.pdb -- MODEL/ENDMDL delineated loop/turn interactions for Pascal
7 dssr-2ndstrs.bpseq -- secondary structures in bpseq format
8 dssr-2ndstrs.ct -- secondary structures in connect format
9 dssr-2ndstrs.dbn -- secondary structures in dot-bracket notation
10 dssr-torsions.txt -- Backbone torsion angles and suite names
11 dssr-Uturns.pdb -- MODEL/ENDMDL delineated U-turn motifs
12 dssr-a2bases.pdb -- MODEL/ENDMDL delineated atom-base stacking interactions
at the end of the output file. I was suggesting adding such a feature that would provide easier to
read/parse outputs.
This could be useful also in find_pair for example but seems particularly important in Snap that is a new program.
I suggest to include the line appearing on the screen (saying that the structure contains less than 5 amino acids) in the output of dssr.
Best,
Pascal
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University