Input and runtime details for job 3286210 (precomputed example)

PDB data

	ID of PDB to download and fit		1DXS
	Atom to Fit		CA
	Alternative Atom Identifier		not provided
	Chain identifier		A
	Model identifier		1
Lattice Model

	Lattice Protein Type		no
	Lattice Type		3D face centered cubic (FCC)
	CA-CA bond length		3.8
Method

	Optimization Mode		distance RMSD
	Max to keep per iteration		100
Job ID 3286210 (server version 4.2.1)

	Job Submitted & Queued		@ Mon Jun 13 17:15:10 CEST 2016
	LatFit Started		@ Mon Jun 13 17:15:25 CEST 2016
	LatFit Finished & Post-Processing		@ Mon Jun 13 17:15:25 CEST 2016
	Job Completed		@ Mon Jun 13 17:15:26 CEST 2016
DIRECT ACCESS: http://cpsp.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3286210&toolName=LatFit ( 30 days expiry )
Description of the job

backbone example
Exemplifies the fitting of a backbone-only lattice protein within the FCC lattice.
Output download complete results [zip]

The lattice protein model was fitted to the original data with a
cRMSD = 1.58448 Angstroms
dRMSD = 1.25507 Angstroms
In the following PDB output file of LatFit is visualized, which contains both the original data fitted (chain P in gray) as well as the lattice protein model (chain L in blue). The original PDB file is shown below.
This visualization is created with glmol.
PDB representation of the shown structures

HEADER    LATTICE PROTEIN STRUCTURE               13-JUN-:6   1DXS              
TITLE     FIT OF THE PDB STRUCTURE 1DXS ONTO A LATTICE                          
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: LATTICE PROTEIN;                                           
COMPND   3 CHAIN: L, P;                                                         
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1                                                             
KEYWDS    LATTICE FITTING                                                       
EXPDTA    THEORETICAL MODEL                                                     
AUTHOR    LATFIT SOFTWARE                                                       
REMARK  40                                                                      
REMARK  40 GENERATED WITH LATFIT (C) MARTIN MANN 2008                           
REMARK  40  LATTICE = fcc                                                       
REMARK  40  PDB ID  = 1DXS                                                      
REMARK  40  CRMSD   =   1.5845                                                  
REMARK  40  DRMSD   =   1.2551                                                  
REMARK 220                                                                      
REMARK 220 EXPERIMENTAL DETAILS                                                 
REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING                              
REMARK 220                                                                      
REMARK 220 PARAMETER SET APPLIED TO LATFIT :                                    
REMARK 220                                                                      
REMARK 220  pdb-file=input.pdb                                                  
REMARK 220  pdb-chain=A                                                         
REMARK 220  pdb-chain-gaps=true                                                 
REMARK 220  pdb-atom=CA                                                         
REMARK 220  pdb-model=1                                                         
REMARK 220  lattice=fcc                                                         
REMARK 220  bond-len=3.8                                                        
REMARK 220  nKeep=100                                                           
REMARK 220  optimizing=dRMSD                                                    
REMARK 220  side-chain=false                                                    
REMARK 220  sc-lattice=fcc                                                      
REMARK 220  sc-contrib=1                                                        
REMARK 220  fit-dir-vec=false                                                   
REMARK 220  dirVecLength=3.8                                                    
REMARK 220  outOrigData=true                                                    
REMARK 220  outMode=PDB                                                         
REMARK 220                                                                      
REMARK 220 REMARK: THE LATTICE STRUCTURE WAS FITTED USING A GREEDY METHOD       
REMARK 225                                                                      
REMARK 225 THEORETICAL MODEL                                                    
REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A LATTICE MODEL STRUCTURE.   
REMARK 225                                                                      
REMARK 225 THE LATTICE PROTEIN STRUCTURE IS GIVEN AS CHAIN L.                   
REMARK 225 THE BACKBONE IS REPRESENTED BY A CA-ATOMS AS A 'C'-elements.         
REMARK 225                                                                      
REMARK 225 THE INITIAL PROTEIN POSITIONS THAT WERE FITTED ARE GIVEN AS CHAIN P. 
REMARK 225                                                                      
SEQRES   1 L   57  SER LEU VAL SER PHE LEU THR GLY LEU GLY CYS PRO ASN
SEQRES   2 L   57  CYS ILE GLU TYR PHE THR SER GLN GLY LEU GLN SER ILE
SEQRES   3 L   57  TYR HIS LEU GLN ASN LEU THR ILE GLU ASP LEU GLY ALA
SEQRES   4 L   57  LEU LYS ILE PRO GLU GLN TYR ARG MET THR ILE TRP ARG
SEQRES   5 L   57  GLY LEU GLN ASP LEU
SEQRES   1 P   57  SER LEU VAL SER PHE LEU THR GLY LEU GLY CYS PRO ASN
SEQRES   2 P   57  CYS ILE GLU TYR PHE THR SER GLN GLY LEU GLN SER ILE
SEQRES   3 P   57  TYR HIS LEU GLN ASN LEU THR ILE GLU ASP LEU GLY ALA
SEQRES   4 P   57  LEU LYS ILE PRO GLU GLN TYR ARG MET THR ILE TRP ARG
SEQRES   5 P   57  GLY LEU GLN ASP LEU
HETATM    1  CA  SER L   6      27.334  17.039  34.646  1.00  0.00           C  
HETATM    2  CA  LEU L   7      25.380  16.932  31.389  1.00  0.00           C  
HETATM    3  CA  VAL L   8      23.572  16.504  34.703  1.00  0.00           C  
HETATM    4  CA  SER L   9      25.043  19.786  35.930  1.00  0.00           C  
HETATM    5  CA  PHE L  10      23.089  19.679  32.673  1.00  0.00           C  
HETATM    6  CA  LEU L  11      19.328  19.143  32.730  1.00  0.00           C  
HETATM    7  CA  THR L  12      20.798  22.425  33.956  1.00  0.00           C  
HETATM    8  CA  GLY L  13      22.269  25.707  35.183  1.00  0.00           C  
HETATM    9  CA  LEU L  14      20.315  25.600  31.925  1.00  0.00           C  
HETATM   10  CA  GLY L  15      16.554  25.065  31.983  1.00  0.00           C  
HETATM   11  CA  CYS L  16      15.083  21.783  30.756  1.00  0.00           C  
HETATM   12  CA  PRO L  17      15.566  18.607  32.787  1.00  0.00           C  
HETATM   13  CA  ASN L  18      13.612  18.500  29.529  1.00  0.00           C  
HETATM   14  CA  CYS L  19      15.903  15.754  28.246  1.00  0.00           C  
HETATM   15  CA  ILE L  20      19.665  16.290  28.188  1.00  0.00           C  
HETATM   16  CA  GLU L  21      18.194  13.007  26.962  1.00  0.00           C  
HETATM   17  CA  TYR L  22      16.241  12.900  23.704  1.00  0.00           C  
HETATM   18  CA  PHE L  23      20.002  13.436  23.647  1.00  0.00           C  
HETATM   19  CA  THR L  24      20.485  10.261  25.678  1.00  0.00           C  
HETATM   20  CA  SER L  25      18.532  10.154  22.420  1.00  0.00           C  
HETATM   21  CA  GLN L  26      20.823   7.407  21.137  1.00  0.00           C  
HETATM   22  CA  GLY L  27      22.776   7.514  24.394  1.00  0.00           C  
HETATM   23  CA  LEU L  28      24.247  10.797  25.621  1.00  0.00           C  
HETATM   24  CA  GLN L  29      26.201  10.904  28.878  1.00  0.00           C  
HETATM   25  CA  SER L  30      29.962  11.439  28.821  1.00  0.00           C  
HETATM   26  CA  ILE L  31      29.479  14.614  26.790  1.00  0.00           C  
HETATM   27  CA  TYR L  32      33.241  15.150  26.733  1.00  0.00           C  
HETATM   28  CA  HIS L  33      31.287  15.043  23.475  1.00  0.00           C  
HETATM   29  CA  LEU L  34      28.996  17.790  24.759  1.00  0.00           C  
HETATM   30  CA  GLN L  35      30.804  18.218  21.444  1.00  0.00           C  
HETATM   31  CA  ASN L  36      32.612  18.647  18.130  1.00  0.00           C  
HETATM   32  CA  LEU L  37      28.850  18.111  18.187  1.00  0.00           C  
HETATM   33  CA  THR L  38      28.367  21.287  16.156  1.00  0.00           C  
HETATM   34  CA  ILE L  39      24.606  20.751  16.213  1.00  0.00           C  
HETATM   35  CA  GLU L  40      22.652  20.644  12.956  1.00  0.00           C  
HETATM   36  CA  ASP L  41      23.135  17.469  14.987  1.00  0.00           C  
HETATM   37  CA  LEU L  42      20.844  20.215  16.270  1.00  0.00           C  
HETATM   38  CA  GLY L  43      17.083  19.680  16.328  1.00  0.00           C  
HETATM   39  CA  ALA L  44      19.373  16.933  15.044  1.00  0.00           C  
HETATM   40  CA  LEU L  45      17.566  16.504  18.359  1.00  0.00           C  
HETATM   41  CA  LYS L  46      13.804  15.969  18.416  1.00  0.00           C  
HETATM   42  CA  ILE L  47      15.275  19.251  19.642  1.00  0.00           C  
HETATM   43  CA  PRO L  48      12.984  21.997  20.926  1.00  0.00           C  
HETATM   44  CA  GLU L  49      12.501  25.173  18.895  1.00  0.00           C  
HETATM   45  CA  GLN L  50      14.454  25.280  22.153  1.00  0.00           C  
HETATM   46  CA  TYR L  51      16.408  25.386  25.410  1.00  0.00           C  
HETATM   47  CA  ARG L  52      18.216  25.815  22.096  1.00  0.00           C  
HETATM   48  CA  MET L  53      21.978  26.351  22.038  1.00  0.00           C  
HETATM   49  CA  THR L  54      20.170  25.922  25.353  1.00  0.00           C  
HETATM   50  CA  ILE L  55      22.461  23.176  24.069  1.00  0.00           C  
HETATM   51  CA  TRP L  56      24.268  23.604  20.754  1.00  0.00           C  
HETATM   52  CA  ARG L  57      25.739  26.887  21.981  1.00  0.00           C  
HETATM   53  CA  GLY L  58      27.693  26.993  25.239  1.00  0.00           C  
HETATM   54  CA  LEU L  59      29.984  24.247  23.955  1.00  0.00           C  
HETATM   55  CA  GLN L  60      29.501  27.422  21.924  1.00  0.00           C  
HETATM   56  CA  ASP L  61      31.454  27.529  25.181  1.00  0.00           C  
HETATM   57  CA  LEU L  62      31.938  24.354  27.212  1.00  0.00           C  
HETATM   58  CA  SER P   6      27.815  16.739  34.595  1.00  0.00           C  
HETATM   59  CA  LEU P   7      25.449  16.151  31.669  1.00  0.00           C  
HETATM   60  CA  VAL P   8      22.495  16.030  34.030  1.00  0.00           C  
HETATM   61  CA  SER P   9      23.685  19.112  35.903  1.00  0.00           C  
HETATM   62  CA  PHE P  10      24.525  20.878  32.657  1.00  0.00           C  
HETATM   63  CA  LEU P  11      21.050  20.724  31.095  1.00  0.00           C  
HETATM   64  CA  THR P  12      19.518  21.505  34.493  1.00  0.00           C  
HETATM   65  CA  GLY P  13      21.700  24.524  35.295  1.00  0.00           C  
HETATM   66  CA  LEU P  14      20.772  25.716  31.811  1.00  0.00           C  
HETATM   67  CA  GLY P  15      17.099  25.233  32.599  1.00  0.00           C  
HETATM   68  CA  CYS P  16      16.294  22.315  30.254  1.00  0.00           C  
HETATM   69  CA  PRO P  17      16.406  18.950  32.131  1.00  0.00           C  
HETATM   70  CA  ASN P  18      13.624  17.972  29.757  1.00  0.00           C  
HETATM   71  CA  CYS P  19      16.263  17.919  27.043  1.00  0.00           C  
HETATM   72  CA  ILE P  20      18.207  15.251  28.898  1.00  0.00           C  
HETATM   73  CA  GLU P  21      16.281  12.370  27.389  1.00  0.00           C  
HETATM   74  CA  TYR P  22      17.184  13.479  23.872  1.00  0.00           C  
HETATM   75  CA  PHE P  23      20.838  12.723  24.490  1.00  0.00           C  
HETATM   76  CA  THR P  24      20.669   9.744  26.849  1.00  0.00           C  
HETATM   77  CA  SER P  25      18.198   8.252  24.411  1.00  0.00           C  
HETATM   78  CA  GLN P  26      21.031   7.999  21.873  1.00  0.00           C  
HETATM   79  CA  GLY P  27      23.646   6.837  24.349  1.00  0.00           C  
HETATM   80  CA  LEU P  28      25.074  10.322  24.785  1.00  0.00           C  
HETATM   81  CA  GLN P  29      26.149  10.829  28.394  1.00  0.00           C  
HETATM   82  CA  SER P  30      29.553  12.515  28.091  1.00  0.00           C  
HETATM   83  CA  ILE P  31      30.313  16.216  27.872  1.00  0.00           C  
HETATM   84  CA  TYR P  32      33.274  15.714  25.516  1.00  0.00           C  
HETATM   85  CA  HIS P  33      31.297  14.080  22.740  1.00  0.00           C  
HETATM   86  CA  LEU P  34      28.508  16.559  23.372  1.00  0.00           C  
HETATM   87  CA  GLN P  35      30.746  19.493  22.376  1.00  0.00           C  
HETATM   88  CA  ASN P  36      31.420  18.465  18.776  1.00  0.00           C  
HETATM   89  CA  LEU P  37      27.728  18.296  17.873  1.00  0.00           C  
HETATM   90  CA  THR P  38      26.412  20.911  15.466  1.00  0.00           C  
HETATM   91  CA  ILE P  39      23.349  23.104  15.603  1.00  0.00           C  
HETATM   92  CA  GLU P  40      21.962  20.816  12.891  1.00  0.00           C  
HETATM   93  CA  ASP P  41      22.775  17.781  15.043  1.00  0.00           C  
HETATM   94  CA  LEU P  42      20.708  19.197  17.907  1.00  0.00           C  
HETATM   95  CA  GLY P  43      17.878  19.519  15.435  1.00  0.00           C  
HETATM   96  CA  ALA P  44      18.266  15.929  14.253  1.00  0.00           C  
HETATM   97  CA  LEU P  45      18.169  14.887  17.915  1.00  0.00           C  
HETATM   98  CA  LYS P  46      14.587  16.226  17.887  1.00  0.00           C  
HETATM   99  CA  ILE P  47      15.520  18.908  20.432  1.00  0.00           C  
HETATM  100  CA  PRO P  48      12.998  21.767  20.860  1.00  0.00           C  
HETATM  101  CA  GLU P  49      13.969  24.781  18.725  1.00  0.00           C  
HETATM  102  CA  GLN P  50      13.726  26.718  21.977  1.00  0.00           C  
HETATM  103  CA  TYR P  51      16.775  25.212  23.682  1.00  0.00           C  
HETATM  104  CA  ARG P  52      18.951  24.564  20.680  1.00  0.00           C  
HETATM  105  CA  MET P  53      21.190  27.662  20.828  1.00  0.00           C  
HETATM  106  CA  THR P  54      20.973  27.715  24.614  1.00  0.00           C  
HETATM  107  CA  ILE P  55      22.491  24.249  24.705  1.00  0.00           C  
HETATM  108  CA  TRP P  56      24.712  24.818  21.666  1.00  0.00           C  
HETATM  109  CA  ARG P  57      26.029  28.078  23.030  1.00  0.00           C  
HETATM  110  CA  GLY P  58      26.551  26.409  26.415  1.00  0.00           C  
HETATM  111  CA  LEU P  59      28.492  23.493  24.952  1.00  0.00           C  
HETATM  112  CA  GLN P  60      30.710  25.937  23.062  1.00  0.00           C  
HETATM  113  CA  ASP P  61      31.644  27.439  26.414  1.00  0.00           C  
HETATM  114  CA  LEU P  62      33.052  24.014  27.261  1.00  0.00           C  
TER                                                                             
CONECT    1    2                                                                
CONECT    2    1    3                                                           
CONECT    3    2    4                                                           
CONECT    4    3    5                                                           
CONECT    5    4    6                                                           
CONECT    6    5    7                                                           
CONECT    7    6    8                                                           
CONECT    8    7    9                                                           
CONECT    9    8   10                                                           
CONECT   10    9   11                                                           
CONECT   11   10   12                                                           
CONECT   12   11   13                                                           
CONECT   13   12   14                                                           
CONECT   14   13   15                                                           
CONECT   15   14   16                                                           
CONECT   16   15   17                                                           
CONECT   17   16   18                                                           
CONECT   18   17   19                                                           
CONECT   19   18   20                                                           
CONECT   20   19   21                                                           
CONECT   21   20   22                                                           
CONECT   22   21   23                                                           
CONECT   23   22   24                                                           
CONECT   24   23   25                                                           
CONECT   25   24   26                                                           
CONECT   26   25   27                                                           
CONECT   27   26   28                                                           
CONECT   28   27   29                                                           
CONECT   29   28   30                                                           
CONECT   30   29   31                                                           
CONECT   31   30   32                                                           
CONECT   32   31   33                                                           
CONECT   33   32   34                                                           
CONECT   34   33   35                                                           
CONECT   35   34   36                                                           
CONECT   36   35   37                                                           
CONECT   37   36   38                                                           
CONECT   38   37   39                                                           
CONECT   39   38   40                                                           
CONECT   40   39   41                                                           
CONECT   41   40   42                                                           
CONECT   42   41   43                                                           
CONECT   43   42   44                                                           
CONECT   44   43   45                                                           
CONECT   45   44   46                                                           
CONECT   46   45   47                                                           
CONECT   47   46   48                                                           
CONECT   48   47   49                                                           
CONECT   49   48   50                                                           
CONECT   50   49   51                                                           
CONECT   51   50   52                                                           
CONECT   52   51   53                                                           
CONECT   53   52   54                                                           
CONECT   54   53   55                                                           
CONECT   55   54   56                                                           
CONECT   56   55   57                                                           
CONECT   57   56                                                                
CONECT   58   59                                                                
CONECT   59   58   60                                                           
CONECT   60   59   61                                                           
CONECT   61   60   62                                                           
CONECT   62   61   63                                                           
CONECT   63   62   64                                                           
CONECT   64   63   65                                                           
CONECT   65   64   66                                                           
CONECT   66   65   67                                                           
CONECT   67   66   68                                                           
CONECT   68   67   69                                                           
CONECT   69   68   70                                                           
CONECT   70   69   71                                                           
CONECT   71   70   72                                                           
CONECT   72   71   73                                                           
CONECT   73   72   74                                                           
CONECT   74   73   75                                                           
CONECT   75   74   76                                                           
CONECT   76   75   77                                                           
CONECT   77   76   78                                                           
CONECT   78   77   79                                                           
CONECT   79   78   80                                                           
CONECT   80   79   81                                                           
CONECT   81   80   82                                                           
CONECT   82   81   83                                                           
CONECT   83   82   84                                                           
CONECT   84   83   85                                                           
CONECT   85   84   86                                                           
CONECT   86   85   87                                                           
CONECT   87   86   88                                                           
CONECT   88   87   89                                                           
CONECT   89   88   90                                                           
CONECT   90   89   91                                                           
CONECT   91   90   92                                                           
CONECT   92   91   93                                                           
CONECT   93   92   94                                                           
CONECT   94   93   95                                                           
CONECT   95   94   96                                                           
CONECT   96   95   97                                                           
CONECT   97   96   98                                                           
CONECT   98   97   99                                                           
CONECT   99   98  100                                                           
CONECT  100   99  101                                                           
CONECT  101  100  102                                                           
CONECT  102  101  103                                                           
CONECT  103  102  104                                                           
CONECT  104  103  105                                                           
CONECT  105  104  106                                                           
CONECT  106  105  107                                                           
CONECT  107  106  108                                                           
CONECT  108  107  109                                                           
CONECT  109  108  110                                                           
CONECT  110  109  111                                                           
CONECT  111  110  112                                                           
CONECT  112  111  113                                                           
CONECT  113  112  114                                                           
CONECT  114  113                                                                
END
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When using LatFit please cite :

Martin Mann, Rhodri Saunders, Cameron Smith, Rolf Backofen, Charlotte M. Deane
Producing high-accuracy lattice models from protein atomic co-ordinates including side chains
Advances in Bioinformatics, Article ID 148045, 6, 2012
Martin Mann, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, and Rolf Backofen
CPSP-web-tools: a server for 3D lattice protein studies
Bioinformatics, 25 (5), 676-677, 2009
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