Output from STAMP database scanning mode

Output from STAMP scans consists of a list of domains and a corresponding set of scores, lengths and other numbers that can be used to sort and understand the output.

The format is as follows (see examples/ig/stamp_scan.trans):

    % Output from STAMP scanning routine
    %
    % Domain 2fb4lv was used to scan the domain database:
    %  some.domains
    % 1 fits were performed
    % Fit 1 E1= 20.000, E2=  3.800, CUT=  1.000
    % Approximate fits (alignment from N-termini) were performed
    %   at every 10 residue of the database sequences 
    % Transformations were output for Sc=  2.000
    % 
    % Domain used to scan 
    # Sc= 10.000 RMS=  0.01  Len= 999 nfit= 999 Seqid= 100.00 Secid= 100.00 q_len=  111 d_len=  111 n_sec= 100 n_equiv 999 fit_pos= _  0 _ 
    ./pdb2fb4.ent 2fb4lv { L 1 _ to L 109 _  }
    # Sc=   4.332 RMS=   1.556 len=  123 nfit=   57 seq_id= 21.82 sec_id= 74.55 q_len=  111 d_len=  105 n_sec=   10 n_equiv=   55 fit_pos= L 110 _ 
    /db/pdb_all//2fb4.pdb 2fb4lc_1 {  L 110 _ to L 214 _  
    -0.69582   -0.69016    0.19878       132.36090 
    -0.57870    0.37482   -0.72430        67.11302 
    0.42538   -0.61902   -0.66021       109.94639  }
    # Sc=   9.799 RMS=   0.001 len=  111 nfit=  111 seq_id= 100.00 sec_id= 97.30 q_len=  111 d_len=  216 n_sec=   11 n_equiv=  111 fit_pos= L   1 _ 
    /db/pdb_all//2fb4.pdb 2fb4l_1 {  CHAIN L  
    1.00000    0.00001   -0.00002         0.00194 
    -0.00001    1.00000    0.00000         0.00193 
    0.00002   -0.00000    1.00000        -0.00027  }
    # Sc=   7.842 RMS=   1.128 len=  116 nfit=   95 seq_id= 48.94 sec_id= 86.17 q_len=  111 d_len=  113 n_sec=   11 n_equiv=   94 fit_pos= L   1 _ 
    /db/pdb_all//1mcp.pdb 1mcplv_1 {  L 1 _ to L 113 _  
    -0.54068    0.77937    0.31662        37.59489 
    0.79918    0.35840    0.48255         0.56629 
    0.26261    0.51394   -0.81664       -33.14809  }
    <etc.>

(note that the lines beginning with `#' symbols have been wrapped here) `%` denotes a comment, and `#' denotes numbers corresponding to the domain description described below (both will be ignored by all programs except for SORTTRANS, which uses the `#' fields to sort and interpret the data.

`Sc' is the STAMP Score for the comparison of the query to each database sequence. `RMS' is the RMS difference between equivalenced atoms, `len' is the alignment length, `nfit' is the number of atoms used during the final fit of the two domains, `seq_id' and `sec_id' are the sequence and secondary structure identities, `q_len' and `d_len' are the lengths of the query and database structure (in residues), `n_sec' is the number of equivalenced secondary structures, and `n_equiv' are the number of residues found within stretches of 3 or more having $P_{ij}^{\prime} \geq 6$. These fields are used during any run of SORTTRANS to sort and remove redundant/poor superimpositions. `fit_pos' is the Brookhaven numbering of the position in the database sequence to which the query's N-terminal end was aligned for the initial fit. The transformation supplied is that for the superimposition of the database structures onto the query.