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PP Help 06: Advanced output options

ADVANCED OUTPUT OPTIONS

The following output options have been implemented (most of the options are mutually not exclusive, i.e. you can add most of these additional keywords at the same time).

General output options

1. Store results here, return no mail output ('return no mail')
   The string "return no mail" in any line before the one starting with a hash (#) results in that we shall not returned the results by mail. Instead, the results for your requests will be stored on our machines for 3 days, and you will receive a mail that simply tells you how you can ftp the result from here. The reason for including this option is that some requests may result in very large output files, and those may be difficult to handle for your local mailing device (in particular when you request HTML formatted output).
2. Return results in HTML ('return html')
   The string "return html" in any line before the one starting with a hash (#) results in that the email you get will have the entire results attached in one HTML formatted file (which you can load into any WWW browser).
   
   • Alignments and ProDom results are displayed using the program MView developed by (A HREF="http://mathbio.nimr.mrc.ac.uk/~nbrown/">Nigel Brown (MRC, Mill Hill, London).
   • All other results is still simply converted to a format resembling the old output. (I hope that this is going to change soon.)
3. Return output in HTML format for printouts ('perline=60')
   The strings "return html 60" OR "perline=N" (with N=1..number of residues of your protein) in any line before the one starting with a hash (#) result in that the email you get will have the all output attached in one HTML formatted file (to display with any WWW browser) that has fewer characters per line than the normal HTML output (see "return HTML"), so that you can print the output. (For further information see the option "return html".)
4. Return output in HTML (with PHD graphics) ('return html detail')
   The string "return html detail" in any line before the one starting with a hash (#) results in that the email you get will have the entire results attached in one HTML formatted file (which you can load into any WWW browser).
   • Note: the HTML files resulting from the PHD predictions may be large. To avoid that your mail will be too big, you may therefore use the option of leaving the result on our machines, and simply ftp it to your local machine (see option "return no mail").
5. Return HTML (with PHD graphics) for printouts ('perline=60')
   The strings "return html detail 60" OR "perline=N" (with N=1..number of residues of your protein) in any line before the one starting with a hash (#) result in that the email you get will have the all output attached in one HTML formatted file (to display with any WWW browser) that has fewer characters per line than the normal HTML output (see "return HTML detail"), so that you can print the output. (For further information see the option "return html".)
   • Note: the HTML files resulting from the PHD predictions may be large. To avoid that your mail will be too big, you may therefore use the option of leaving the result on our machines, and simply ftp it to your local machine (see option "return no mail").
   
   
6. Return concise output ('return concise')
   The string "return concise result" in any line before the one starting with a hash (#) returns a concise summary of results (e.g., no tables for prediction accuracy).

Customising alignment

1. Return also BLASTP output ('return blast')
   The string "return blast" in any line before the one starting with a hash (#) returns additionally the unfiltered BLASTP output.
2. Return no alignment ('return no alignment')
   The string "return no alignment" in any line before the one starting with a hash (#) returns no alignment.
3. Return alignment in MSF format ('return msf' = default return format)
   The string "return msf" in any line before the one starting with a hash (#) returns the HSSP/MaxHom alignment in MSF format. (Note: this format can be used as input for a request of homology modelling.)
4. Return alignment in HSSP format without profiles ('return hssp format')
   The string "return hssp format" in any line before the one starting with a hash (#) return the HSSP/MaxHom alignment without profiles of residue substitution frequencies (default MSF format without profiles).
5. Return alignment in HSSP format + profiles ('return hssp profiles')
   The string "return hssp profiles" in any line before the one starting with a hash (#) return the HSSP/MaxHom alignment including profiles of residue substitution frequencies (default MSF format without profiles).
6. Report full sequences in alignment returned ('return ali full')
   The string "return ali full" in any line before the one starting with a hash (#) results in that the HSSP/MaxHom alignment returned contain the full sequences of the aligned proteins (default MSF format with deletions in aligned proteins).

Customising PHD

1. Return COLUMN format ("return column format")
   The string "return column format" in any line before the one starting with a hash (#) returns the secondary structure and accessibility predictions in a column format. (Note: this format can be used as input for a request of prediction-based threading.)
2. Return prediction additionally in MSF format ("return phd msf")
   The string "return phd msf" in any line before the one starting with a hash (#) returns the PHD predictions additionally in an MSF format (appended to the alignment).
3. Return prediction additionally in RDB format ("return phd rdb")
   The string "return phd rdb" in any line before the one starting with a hash (#) returns the PHD predictions additionally in RDB format (as read and written by local versions of the programs PHD and TOPITS).
4. Return prediction additionally in CASP2 format ("return phd casp2")
   The string "return phd casp2" in any line before the one starting with a hash (#) returns the PHD predictions additionally in the format used for the second protein structure prediction contest in Asilomar, 1996 (CASP2).
   
5. Return prediction probability for graphical display ("return graph")
   The string "return graph" in any line before the one starting with a hash (#) append a file containing the 1D structure prediction in such a format that the relative propensities for the prediction of each of the output states (e.g. three secondary structure types: helix, strand, rest) can be used as input for usual graphics software (if appropriately extracted), such as KaleidaGraph, Excel, Mathematica, Sigma-Plot, Harvard-Graphics. Example:

   ridiculase (17 residues)
     No,AA,PSEC,RI_S,OtH,OtE,OtL,PACC,PREL,RI_A,Pbie,Ot0,Ot1,..,Ot9
      1, E,   L,   9,  0,  1, 97, 157,  81,   6,   e,  0,  1,.., 21
      2, F,   L,   9,  0,  1, 97,   0,   0,   0,   b,  8,  8,..,  5
      :, :,   :,   :,  :,  :,  :,   :,   :,   :,   :,  :,  :,..,  :
      8, V,   H,   3, 51, 30, 14,   0,   0,   9,   b, 39, 29,..,  1
      9, L,   H,   4, 53, 20, 21,   0,   0,   7,   b, 36, 28,..,  1
     10, R,   H,   1, 36, 32, 24,  62,  25,   1,   i,  8,  8,..,  4
      :, :,   :,   :,  :,  :,  :,   :,   :,   :,   :,  :,  :,..,  :
     16, P,   L,   9,  4,  2, 91,  66,  49,   4,   e,  4,  4,.., 11
     17, A,   L,   9,  2,  1, 95,  51,  49,   2,   e,  7,  7,..,  8
   

Customising TOPITS

1. Return topits hssp ("return topits hssp")
   The string "return topits hssp" in any line before the one starting with a hash (#) returns the threading output additionally in HSSP format.
2. Return topits strip ("return topits strip")
   The string "return topits strip" in any line before the one starting with a hash (#) returns the threading output additionally in STRIP format (which displays predicted and observed secondary structure underneath one another).
3. Return topits own ("return topits own")
   The string "return topits own" in any line before the one starting with a hash (#) returns the threading output additionally in the format used by TOPITS.

Toggle defaults

1. Return no coils ("return no coils")
   The string "return no coils" in any line before the one starting with a hash (#) results in that COILS results are not returned.
   Note: to explicitly REQUEST Coils predictions use the string "do coils".
2. Return no ProSite ("return no ProSite")
   The string "return no ProSite" in any line before the one starting with a hash (#) results in that ProSite results are not returned.
   Note: to explicitly REQUEST detection of ProSite motifs use the string "do prosite".
3. Return no prodom ("return no prodom")
   The string "return no prodom" in any line before the one starting with a hash (#) results in that ProDom results are not returned.
   Note: to explicitly REQUEST ProDom domain assignments use the string "do prodom".
4. Return no seg ('return no seg')
   The string "return no seg" in any line before the one starting with a hash (#) results in that SEG results are not returned. Note: to explicitly REQUEST SEG framing use the string "do seg".

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