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Author Topic: small requests  (Read 5875 times)

Offline auffinger

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small requests
« on: July 20, 2014, 01:36:59 pm »
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
pascal auffinger
ibmc-cnrs
15, rue rené descartes
67084 strasbourg cedex
france

web sites:
http://www-ibmc.u-strasbg.fr/arn/Westho ... er_pub.HTM
http://www-ibmc.u-

Offline xiangjun

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Re: small requests
« Reply #1 on: July 20, 2014, 07:42:03 pm »
Hi Pascal,

Quote
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 to achieve your goal. For example,

Code: [Select]
x3dna-dssr -i=1ehz.pdb -o=1ehz.out 2> msg
Quote
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
« Last Edit: July 20, 2014, 07:44:05 pm by xiangjun »

Offline auffinger

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Re: small requests
« Reply #2 on: July 21, 2014, 02:35:24 am »
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

 ****************************************************************************
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
pascal auffinger
ibmc-cnrs
15, rue rené descartes
67084 strasbourg cedex
france

web sites:
http://www-ibmc.u-strasbg.fr/arn/Westho ... er_pub.HTM
http://www-ibmc.u-

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.