Output from SCANS

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/1cmsN_stamp_scan.trans):

% Output from STAMP scanning routine
%
% Domain 1cmsN was used to scan the domain database:
%  ac_prot.domains
% 2 fits were performed
% Fit 1 E1= 20.000, E2=  3.800, CUT=  1.000
% Fit 2 E1=  3.800, E2=  3.800, CUT=  4.500
% Approximate fits (alignment from N-termini) were performed
%   at every 5 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=  175 d_len=  175 
          n_sec= 100 n_equiv 999 fit_pos= _  0 _ 
/disk3/pdb/pdb1cms.ent 1cmsN { _ 1 _ to _ 175 _  }
# Sc=   9.744 RMS=   0.000 len=  174 nfit=  174 seq_id= 99.43 sec_id= 94.86 q_len=  175 d_len=  175 
         n_sec=   18 n_equiv=  173 fit_pos= _   1 _ 
/disk3/pdb/pdb1cms.ent 1cmsN_1 {  _ 1 _ to _ 175 _  
   1.00000    0.00000    0.00000         0.00000 
   0.00000    1.00000    0.00000         0.00000 
   0.00000    0.00000    1.00000         0.00000  }
# Sc=   2.749 RMS=   2.352 len=  204 nfit=   63 seq_id=  8.00 sec_id= 41.14 q_len=  175 d_len=  148 
        n_sec=   13 n_equiv=   58 fit_pos= _ 176 _ 
/disk3/pdb/pdb1cms.ent 1cmsC_1 {  _ 176 _ to _ 323 _  
  -0.98340   -0.10624   -0.14708        36.75176 
			<etc.>

(note that the lines begining by `#' 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.