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Outputs


 

LSim processes the job comand file, e.g. job.cmd, and outputs to a file named job.out. The output files look like:

---------------------------------------------------------------------------------
  LSIM LOG FILE
  LSim v 1.0, (C) Pere Constans 2001
  A Quantum Macromolecular Similarity Program
---------------------------------------------------------------------------------

Processing job.cmd

/gscan /Bpdb /nmax=10

Molecular Files Processing
Mol 1MBS  Nat=   1223  Zaa=   6185.77  Bn=  30.0  Bx=  30.0  Bm=  30.0  Dc=  5.38
Mol 1SCT  Nat=   1134  Zaa=   6953.30  Bn=  11.5  Bx=  50.3  Bm=  23.2  Dc=  6.12

Macromolecular Similarity Processing

Pair Similarity  Z(1MBS,1SCT)
Visualization files:     ls_1MBS.pdb   ls_1MBS_1SCT.pdb   ls_1MBS_1SCT.crd
Visualization: vmd -startup ls_1MBS_1SCT.vmd
Global Search: Niter=   1521
Local Search:  TIter=    313     AvIter=   31     MaxFound=   9     MaxNoRep=   9

C(AB000)=      0.453       d(AB000)=     84.844
C(AB001)=      0.365       d(AB001)=     91.410
C(AB002)=      0.352       d(AB002)=     92.346
C(AB003)=      0.347       d(AB003)=     92.635
C(AB004)=      0.347       d(AB004)=     92.677
C(AB005)=      0.344       d(AB005)=     92.857
C(AB006)=      0.341       d(AB006)=     93.088
C(AB007)=      0.340       d(AB007)=     93.169
C(AB008)=      0.312       d(AB008)=     95.097


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  END LSIM LOG FILE
--------------------------------------------------------------------------------- 

The output file prompts the similarity indices and molecular distances, while the aligned coordinates are stored in sets of ls_*.pdb files. Each file contains a single structure. In the example, ls_1MBS.pdb stores the 1MBS coordinates at the LSim standard orientation, and ls_1MBS_1SCT.pdb stores the 1SCT coordinates aligned with respect ls_1MBS. Multiple, local alignments are stored as trajectory files ls_*.crd. For convenience, a VMD script is also generated. Visualization of a single or multiple, local alignments is feasible by typing the command:

vmd -startup ls_1MBS_1SCT.vmd