Clustering issue

[Anonymous]

Dear all,

 

I am using Calibur to create my clusters. I dont understand the output.

It shows there are two large clusters and lists the centroid. Then it goes on showing the content on the largest cluster, but the not the second cluster. Then it lists another 2 clusters. However, why is the second cluster missing?

Also, the total of decoys doesnt add up. It should be 1000 but its much less.

I am a bit confused as to how many clusters do I have in total and where there are listed.

 

Can someone help?

 

iltering on

Signature mode on

Using chains ‘A’, ‘C’, ‘ ‘ in PDB files

Read 1000 decoy names

Estimating threshold range…

Estimating threshold range…  6.2%

Estimating threshold range… 12.5%

Estimating threshold range… 18.8%

Estimating threshold range… 25.0%

Estimating threshold range… 31.2%

Estimating threshold range… 37.5%

Estimating threshold range… 43.8%

Estimating threshold range… 50.0%

Estimating threshold range… 56.2%

Estimating threshold range… 62.5%

Estimating threshold range… 68.8%

Estimating threshold range… 75.0%

Estimating threshold range… 81.2%

Estimating threshold range… 87.5%

Estimating threshold range… 93.8%

Estimating threshold range… 100.0%

Estimating threshold range… complete

Estimated threshold range = [0.98167, 9.42590]

Most frequent distance = 3.39553

10.00000 percent distances below 2.58573

Finding threshold to keep 17.78279% edges

Threshold = 2.58573

Reading decoys with signature mode on and filter mode on

Read 1000 decoys. Filtered 0 outlier decoys.

Decoys read in 3.79000 s

Initialized 1000 decoys.

Use of SCUD’s bound on

Realigning decoys… completed in 0.01000 s

Using MATRIX mode

Auxiliary clustering…

AuxiliaryClustering… completed in 0.72000 s

Finding decoys neighbors…

Finding and removing largest clusters… completed in 0.00000 s

Largest 2 clusters: tt4mwf_d.full.BL07830001_0004_0123.pdb(302), tt4mwf_d.full.BL07830001_0004_0061.pdb(247). Margin = 18.21192%

tt4mwf_d.full.BL07830001_0004_0123.pdb 302: bd4mwf_d.full.BL07830001_0004_0086.pdb    am4mwf_d.full.BL07830001_0004_0089.pdb    aq4mwf_d.full.BL07830001_0004_0197.pdb    hh4mwf_d.full.BL07830001_0004_0141.pdb    am4mwf_d.full.BL07830001_0004_0061.pdb    bb4mwf_d.full.BL07830001_0004_0168.pdb    az4mwf_d.full.BL07830001_0004_0085.pdb    bq4mwf_d.full.BL07830001_0004_0082.pdb    av4mwf_d.full.BL07830001_0004_0102.pdb    be4mwf_d.full.BL07830001_0004_0016.pdb    bz4mwf_d.full.BL07830001_0004_0119.pdb    bq4mwf_d.full.BL07830001_0004_0057.pdb    ii4mwf_d.full.BL07830001_0004_0136.pdb    mm4mwf_d.full.BL07830001_0004_0033.pdb    ay4mwf_d.full.BL07830001_0004_0178.pdb    bz4mwf_d.full.BL07830001_0004_0110.pdb    ac4mwf_d.full.BL07830001_0004_0134.pdb    ff4mwf_d.full.BL07830001_0004_0105.pdb    ab4mwf_d.full.BL07830001_0004_0012.pdb    gg4mwf_d.full.BL07830001_0004_0174.pdb    ss4mwf_d.full.BL07830001_0004_0188.pdb    az4mwf_d.full.BL07830001_0004_0073.pdb    ae4mwf_d.full.BL07830001_0004_0087.pdb    az4mwf_d.full.BL07830001_0004_0096.pdb    ah4mwf_d.full.BL07830001_0004_0171.pdb    bc4mwf_d.full.BL07830001_0004_0013.pdb    ad4mwf_d.full.BL07830001_0004_0024.pdb    ar4mwf_d.full.BL07830001_0004_0069.pdb    ll4mwf_d.full.BL07830001_0004_0104.pdb    yy4mwf_d.full.BL07830001_0004_0067.pdb    rr4mwf_d.full.BL07830001_0004_0133.pdb    ba4mwf_d.full.BL07830001_0004_0028.pdb    hh4mwf_d.full.BL07830001_0004_0160.pdb    nn4mwf_d.full.BL07830001_0004_0094.pdb    hh4mwf_d.full.BL07830001_0004_0145.pdb    ba4mwf_d.full.BL07830001_0004_0010.pdb    rr4mwf_d.full.BL07830001_0004_0018.pdb    ax4mwf_d.full.BL07830001_0004_0069.pdb    pp4mwf_d.full.BL07830001_0004_0073.pdb    av4mwf_d.full.BL07830001_0004_0199.pdb    ap4mwf_d.full.BL07830001_0004_0056.pdb    kk4mwf_d.full.BL07830001_0004_0130.pdb    mm4mwf_d.full.BL07830001_0004_0062.pdb    ab4mwf_d.full.BL07830001_0004_0003.pdb    ay4mwf_d.full.BL07830001_0004_0055.pdb    am4mwf_d.full.BL07830001_0004_0128.pdb    kk4mwf_d.full.BL07830001_0004_0157.pdb    ay4mwf_d.full.BL07830001_0004_0059.pdb    ax4mwf_d.full.BL07830001_0004_0067.pdb    ap4mwf_d.full.BL07830001_0004_0111.pdb    ag4mwf_d.full.BL07830001_0004_0127.pdb    ll4mwf_d.full.BL07830001_0004_0106.pdb    ii4mwf_d.full.BL07830001_0004_0094.pdb    ab4mwf_d.full.BL07830001_0004_0065.pdb    ai4mwf_d.full.BL07830001_0004_0015.pdb    ar4mwf_d.full.BL07830001_0004_0036.pdb    ba4mwf_d.full.BL07830001_0004_0129.pdb    aq4mwf_d.full.BL07830001_0004_0015.pdb    bz4mwf_d.full.BL07830001_0004_0036.pdb    ax4mwf_d.full.BL07830001_0004_0063.pdb    mm4mwf_d.full.BL07830001_0004_0182.pdb    bb4mwf_d.full.BL07830001_0004_0198.pdb    ag4mwf_d.full.BL07830001_0004_0060.pdb    ag4mwf_d.full.BL07830001_0004_0168.pdb    yy4mwf_d.full.BL07830001_0004_0070.pdb    kk4mwf_d.full.BL07830001_0004_0050.pdb    ff4mwf_d.full.BL07830001_0004_0023.pdb    nn4mwf_d.full.BL07830001_0004_0009.pdb    be4mwf_d.full.BL07830001_0004_0116.pdb    kk4mwf_d.full.BL07830001_0004_0054.pdb    af4mwf_d.full.BL07830001_0004_0059.pdb    jj4mwf_d.full.BL07830001_0004_0087.pdb    ff4mwf_d.full.BL07830001_0004_0089.pdb    ax4mwf_d.full.BL07830001_0004_0010.pdb    kk4mwf_d.full.BL07830001_0004_0188.pdb    ar4mwf_d.full.BL07830001_0004_0012.pdb    kk4mwf_d.full.BL07830001_0004_0044.pdb    am4mwf_d.full.BL07830001_0004_0070.pdb    bq4mwf_d.full.BL07830001_0004_0092.pdb    bv4mwf_d.full.BL07830001_0004_0142.pdb    ad4mwf_d.full.BL07830001_0004_0116.pdb    jj4mwf_d.full.BL07830001_0004_0119.pdb    am4mwf_d.full.BL07830001_0004_0062.pdb    ak4mwf_d.full.BL07830001_0004_0090.pdb    rr4mwf_d.full.BL07830001_0004_0010.pdb    bb4mwf_d.full.BL07830001_0004_0009.pdb    yy4mwf_d.full.BL07830001_0004_0051.pdb    ao4mwf_d.full.BL07830001_0004_0198.pdb    ad4mwf_d.full.BL07830001_0004_0115.pdb    am4mwf_d.full.BL07830001_0004_0075.pdb    ah4mwf_d.full.BL07830001_0004_0164.pdb    av4mwf_d.full.BL07830001_0004_0008.pdb    mm4mwf_d.full.BL07830001_0004_0009.pdb    al4mwf_d.full.BL07830001_0004_0090.pdb    oo4mwf_d.full.BL07830001_0004_0018.pdb    an4mwf_d.full.BL07830001_0004_0073.pdb    al4mwf_d.full.BL07830001_0004_0111.pdb    ak4mwf_d.full.BL07830001_0004_0113.pdb    bc4mwf_d.full.BL07830001_0004_0116.pdb    ak4mwf_d.full.BL07830001_0004_0046.pdb    az4mwf_d.full.BL07830001_0004_0021.pdb    ah4mwf_d.full.BL07830001_0004_0090.pdb    bv4mwf_d.full.BL07830001_0004_0179.pdb    ii4mwf_d.full.BL07830001_0004_0107.pdb    ai4mwf_d.full.BL07830001_0004_0046.pdb    pp4mwf_d.full.BL07830001_0004_0147.pdb    bz4mwf_d.full.BL07830001_0004_0048.pdb    az4mwf_d.full.BL07830001_0004_0053.pdb    ae4mwf_d.full.BL07830001_0004_0023.pdb    av4mwf_d.full.BL07830001_0004_0020.pdb    ff4mwf_d.full.BL07830001_0004_0134.pdb    ay4mwf_d.full.BL07830001_0004_0071.pdb    oo4mwf_d.full.BL07830001_0004_0118.pdb    zz4mwf_d.full.BL07830001_0004_0153.pdb    as4mwf_d.full.BL07830001_0004_0024.pdb    zz4mwf_d.full.BL07830001_0004_0190.pdb    bc4mwf_d.full.BL07830001_0004_0183.pdb    nn4mwf_d.full.BL07830001_0004_0133.pdb    bv4mwf_d.full.BL07830001_0004_0073.pdb    ay4mwf_d.full.BL07830001_0004_0179.pdb    af4mwf_d.full.BL07830001_0004_0198.pdb    az4mwf_d.full.BL07830001_0004_0032.pdb    am4mwf_d.full.BL07830001_0004_0039.pdb    zz4mwf_d.full.BL07830001_0004_0138.pdb    ao4mwf_d.full.BL07830001_0004_0131.pdb    bb4mwf_d.full.BL07830001_0004_0152.pdb    bb4mwf_d.full.BL07830001_0004_0028.pdb    qq4mwf_d.full.BL07830001_0004_0042.pdb    ba4mwf_d.full.BL07830001_0004_0145.pdb    ar4mwf_d.full.BL07830001_0004_0145.pdb    bd4mwf_d.full.BL07830001_0004_0039.pdb    al4mwf_d.full.BL07830001_0004_0037.pdb    tt4mwf_d.full.BL07830001_0004_0176.pdb    zz4mwf_d.full.BL07830001_0004_0112.pdb    bd4mwf_d.full.BL07830001_0004_0092.pdb    hh4mwf_d.full.BL07830001_0004_0162.pdb    ar4mwf_d.full.BL07830001_0004_0056.pdb    al4mwf_d.full.BL07830001_0004_0066.pdb    ii4mwf_d.full.BL07830001_0004_0188.pdb    ak4mwf_d.full.BL07830001_0004_0154.pdb    ak4mwf_d.full.BL07830001_0004_0065.pdb    bz4mwf_d.full.BL07830001_0004_0042.pdb    bv4mwf_d.full.BL07830001_0004_0157.pdb    yy4mwf_d.full.BL07830001_0004_0168.pdb    bz4mwf_d.full.BL07830001_0004_0149.pdb    ak4mwf_d.full.BL07830001_0004_0131.pdb    bz4mwf_d.full.BL07830001_0004_0021.pdb    tt4mwf_d.full.BL07830001_0004_0123.pdb    bb4mwf_d.full.BL07830001_0004_0194.pdb    az4mwf_d.full.BL07830001_0004_0195.pdb    ad4mwf_d.full.BL07830001_0004_0085.pdb    hh4mwf_d.full.BL07830001_0004_0045.pdb    ag4mwf_d.full.BL07830001_0004_0038.pdb    bd4mwf_d.full.BL07830001_0004_0080.pdb    an4mwf_d.full.BL07830001_0004_0020.pdb    be4mwf_d.full.BL07830001_0004_0089.pdb    ad4mwf_d.full.BL07830001_0004_0151.pdb    bz4mwf_d.full.BL07830001_0004_0129.pdb    ak4mwf_d.full.BL07830001_0004_0135.pdb    az4mwf_d.full.BL07830001_0004_0092.pdb    bq4mwf_d.full.BL07830001_0004_0175.pdb    gg4mwf_d.full.BL07830001_0004_0016.pdb    aq4mwf_d.full.BL07830001_0004_0151.pdb    hh4mwf_d.full.BL07830001_0004_0055.pdb    mm4mwf_d.full.BL07830001_0004_0047.pdb    ay4mwf_d.full.BL07830001_0004_0138.pdb    ab4mwf_d.full.BL07830001_0004_0197.pdb    ag4mwf_d.full.BL07830001_0004_0173.pdb    ai4mwf_d.full.BL07830001_0004_0054.pdb    ad4mwf_d.full.BL07830001_0004_0127.pdb    am4mwf_d.full.BL07830001_0004_0127.pdb    ac4mwf_d.full.BL07830001_0004_0192.pdb    am4mwf_d.full.BL07830001_0004_0150.pdb    ap4mwf_d.full.BL07830001_0004_0165.pdb    ll4mwf_d.full.BL07830001_0004_0153.pdb    aq4mwf_d.full.BL07830001_0004_0196.pdb    ii4mwf_d.full.BL07830001_0004_0113.pdb    ar4mwf_d.full.BL07830001_0004_0148.pdb    aq4mwf_d.full.BL07830001_0004_0033.pdb    bz4mwf_d.full.BL07830001_0004_0175.pdb    nn4mwf_d.full.BL07830001_0004_0115.pdb    ff4mwf_d.full.BL07830001_0004_0004.pdb    pp4mwf_d.full.BL07830001_0004_0032.pdb    ac4mwf_d.full.BL07830001_0004_0043.pdb    bb4mwf_d.full.BL07830001_0004_0081.pdb    jj4mwf_d.full.BL07830001_0004_0072.pdb    af4mwf_d.full.BL07830001_0004_0177.pdb    yy4mwf_d.full.BL07830001_0004_0049.pdb    qq4mwf_d.full.BL07830001_0004_0015.pdb    ah4mwf_d.full.BL07830001_0004_0135.pdb    be4mwf_d.full.BL07830001_0004_0146.pdb    bc4mwf_d.full.BL07830001_0004_0101.pdb    aq4mwf_d.full.BL07830001_0004_0120.pdb    bz4mwf_d.full.BL07830001_0004_0143.pdb    ff4mwf_d.full.BL07830001_0004_0145.pdb    as4mwf_d.full.BL07830001_0004_0056.pdb    ss4mwf_d.full.BL07830001_0004_0138.pdb    ak4mwf_d.full.BL07830001_0004_0181.pdb    an4mwf_d.full.BL07830001_0004_0156.pdb    ff4mwf_d.full.BL07830001_0004_0156.pdb    ab4mwf_d.full.BL07830001_0004_0130.pdb    bv4mwf_d.full.BL07830001_0004_0042.pdb    ab4mwf_d.full.BL07830001_0004_0070.pdb    ag4mwf_d.full.BL07830001_0004_0200.pdb    af4mwf_d.full.BL07830001_0004_0015.pdb    yy4mwf_d.full.BL07830001_0004_0107.pdb    bz4mwf_d.full.BL07830001_0004_0088.pdb    aq4mwf_d.full.BL07830001_0004_0030.pdb    ao4mwf_d.full.BL07830001_0004_0135.pdb    ss4mwf_d.full.BL07830001_0004_0019.pdb    bv4mwf_d.full.BL07830001_0004_0062.pdb    rr4mwf_d.full.BL07830001_0004_0141.pdb    bv4mwf_d.full.BL07830001_0004_0135.pdb    al4mwf_d.full.BL07830001_0004_0025.pdb    ii4mwf_d.full.BL07830001_0004_0088.pdb    ss4mwf_d.full.BL07830001_0004_0117.pdb    jj4mwf_d.full.BL07830001_0004_0193.pdb    ac4mwf_d.full.BL07830001_0004_0096.pdb    gg4mwf_d.full.BL07830001_0004_0025.pdb    gg4mwf_d.full.BL07830001_0004_0151.pdb    kk4mwf_d.full.BL07830001_0004_0136.pdb    al4mwf_d.full.BL07830001_0004_0007.pdb    ai4mwf_d.full.BL07830001_0004_0130.pdb    yy4mwf_d.full.BL07830001_0004_0191.pdb    ah4mwf_d.full.BL07830001_0004_0051.pdb    yy4mwf_d.full.BL07830001_0004_0017.pdb    ag4mwf_d.full.BL07830001_0004_0020.pdb    jj4mwf_d.full.BL07830001_0004_0163.pdb    as4mwf_d.full.BL07830001_0004_0023.pdb    ll4mwf_d.full.BL07830001_0004_0156.pdb    qq4mwf_d.full.BL07830001_0004_0065.pdb    ao4mwf_d.full.BL07830001_0004_0106.pdb    gg4mwf_d.full.BL07830001_0004_0136.pdb    pp4mwf_d.full.BL07830001_0004_0059.pdb    af4mwf_d.full.BL07830001_0004_0181.pdb    bd4mwf_d.full.BL07830001_0004_0008.pdb    ar4mwf_d.full.BL07830001_0004_0115.pdb    bz4mwf_d.full.BL07830001_0004_0034.pdb    ak4mwf_d.full.BL07830001_0004_0036.pdb    oo4mwf_d.full.BL07830001_0004_0055.pdb    zz4mwf_d.full.BL07830001_0004_0145.pdb    av4mwf_d.full.BL07830001_0004_0198.pdb    ac4mwf_d.full.BL07830001_0004_0031.pdb    yy4mwf_d.full.BL07830001_0004_0123.pdb    kk4mwf_d.full.BL07830001_0004_0147.pdb    ak4mwf_d.full.BL07830001_0004_0023.pdb    bc4mwf_d.full.BL07830001_0004_0090.pdb    rr4mwf_d.full.BL07830001_0004_0110.pdb    bb4mwf_d.full.BL07830001_0004_0174.pdb    bq4mwf_d.full.BL07830001_0004_0066.pdb    ay4mwf_d.full.BL07830001_0004_0136.pdb    ff4mwf_d.full.BL07830001_0004_0020.pdb    qq4mwf_d.full.BL07830001_0004_0199.pdb    bz4mwf_d.full.BL07830001_0004_0132.pdb    ba4mwf_d.full.BL07830001_0004_0182.pdb    yy4mwf_d.full.BL07830001_0004_0097.pdb    be4mwf_d.full.BL07830001_0004_0176.pdb    mm4mwf_d.full.BL07830001_0004_0191.pdb    bc4mwf_d.full.BL07830001_0004_0097.pdb    mm4mwf_d.full.BL07830001_0004_0071.pdb    bz4mwf_d.full.BL07830001_0004_0032.pdb    ar4mwf_d.full.BL07830001_0004_0061.pdb    gg4mwf_d.full.BL07830001_0004_0146.pdb    ak4mwf_d.full.BL07830001_0004_0055.pdb    am4mwf_d.full.BL07830001_0004_0177.pdb    mm4mwf_d.full.BL07830001_0004_0193.pdb    jj4mwf_d.full.BL07830001_0004_0114.pdb    ap4mwf_d.full.BL07830001_0004_0095.pdb    bd4mwf_d.full.BL07830001_0004_0009.pdb    af4mwf_d.full.BL07830001_0004_0040.pdb    jj4mwf_d.full.BL07830001_0004_0108.pdb    bc4mwf_d.full.BL07830001_0004_0104.pdb    al4mwf_d.full.BL07830001_0004_0115.pdb    as4mwf_d.full.BL07830001_0004_0175.pdb    af4mwf_d.full.BL07830001_0004_0095.pdb    gg4mwf_d.full.BL07830001_0004_0018.pdb    af4mwf_d.full.BL07830001_0004_0097.pdb    oo4mwf_d.full.BL07830001_0004_0115.pdb    ah4mwf_d.full.BL07830001_0004_0104.pdb    ao4mwf_d.full.BL07830001_0004_0171.pdb    ac4mwf_d.full.BL07830001_0004_0046.pdb    aq4mwf_d.full.BL07830001_0004_0192.pdb    tt4mwf_d.full.BL07830001_0004_0099.pdb    ll4mwf_d.full.BL07830001_0004_0128.pdb    be4mwf_d.full.BL07830001_0004_0145.pdb    oo4mwf_d.full.BL07830001_0004_0075.pdb    ae4mwf_d.full.BL07830001_0004_0158.pdb    ac4mwf_d.full.BL07830001_0004_0152.pdb    tt4mwf_d.full.BL07830001_0004_0173.pdb    am4mwf_d.full.BL07830001_0004_0159.pdb    ah4mwf_d.full.BL07830001_0004_0169.pdb    bb4mwf_d.full.BL07830001_0004_0084.pdb    ax4mwf_d.full.BL07830001_0004_0148.pdb    ak4mwf_d.full.BL07830001_0004_0144.pdb    hh4mwf_d.full.BL07830001_0004_0105.pdb    bd4mwf_d.full.BL07830001_0004_0165.pdb    ap4mwf_d.full.BL07830001_0004_0053.pdb    as4mwf_d.full.BL07830001_0004_0086.pdb    av4mwf_d.full.BL07830001_0004_0123.pdb    bz4mwf_d.full.BL07830001_0004_0184.pdb    av4mwf_d.full.BL07830001_0004_0051.pdb    ll4mwf_d.full.BL07830001_0004_0126.pdb    

tt4mwf_d.full.BL07830001_0004_0061.pdb 174: ac4mwf_d.full.BL07830001_0004_0088.pdb    mm4mwf_d.full.BL07830001_0004_0051.pdb    ak4mwf_d.full.BL07830001_0004_0001.pdb    an4mwf_d.full.BL07830001_0004_0010.pdb    ii4mwf_d.full.BL07830001_0004_0177.pdb    ii4mwf_d.full.BL07830001_0004_0015.pdb    ab4mwf_d.full.BL07830001_0004_0164.pdb    ee4mwf_d.full.BL07830001_0004_0050.pdb    ak4mwf_d.full.BL07830001_0004_0164.pdb    rr4mwf_d.full.BL07830001_0004_0043.pdb    ab4mwf_d.full.BL07830001_0004_0139.pdb    ba4mwf_d.full.BL07830001_0004_0090.pdb    al4mwf_d.full.BL07830001_0004_0189.pdb    bq4mwf_d.full.BL07830001_0004_0048.pdb    yy4mwf_d.full.BL07830001_0004_0120.pdb    aq4mwf_d.full.BL07830001_0004_0039.pdb    ah4mwf_d.full.BL07830001_0004_0101.pdb    bd4mwf_d.full.BL07830001_0004_0007.pdb    qq4mwf_d.full.BL07830001_0004_0178.pdb    tt4mwf_d.full.BL07830001_0004_0061.pdb    bc4mwf_d.full.BL07830001_0004_0144.pdb    ak4mwf_d.full.BL07830001_0004_0100.pdb    ar4mwf_d.full.BL07830001_0004_0184.pdb    ac4mwf_d.full.BL07830001_0004_0057.pdb    ba4mwf_d.full.BL07830001_0004_0032.pdb    bb4mwf_d.full.BL07830001_0004_0146.pdb    ap4mwf_d.full.BL07830001_0004_0045.pdb    ae4mwf_d.full.BL07830001_0004_0065.pdb    ak4mwf_d.full.BL07830001_0004_0104.pdb    al4mwf_d.full.BL07830001_0004_0065.pdb    ac4mwf_d.full.BL07830001_0004_0001.pdb    am4mwf_d.full.BL07830001_0004_0041.pdb    gg4mwf_d.full.BL07830001_0004_0047.pdb    ee4mwf_d.full.BL07830001_0004_0091.pdb    ah4mwf_d.full.BL07830001_0004_0014.pdb    am4mwf_d.full.BL07830001_0004_0081.pdb    ak4mwf_d.full.BL07830001_0004_0140.pdb    bq4mwf_d.full.BL07830001_0004_0086.pdb    oo4mwf_d.full.BL07830001_0004_0192.pdb    aq4mwf_d.full.BL07830001_0004_0100.pdb    aq4mwf_d.full.BL07830001_0004_0036.pdb    mm4mwf_d.full.BL07830001_0004_0048.pdb    pp4mwf_d.full.BL07830001_0004_0193.pdb    ay4mwf_d.full.BL07830001_0004_0011.pdb    az4mwf_d.full.BL07830001_0004_0112.pdb    af4mwf_d.full.BL07830001_0004_0082.pdb    nn4mwf_d.full.BL07830001_0004_0046.pdb    ao4mwf_d.full.BL07830001_0004_0011.pdb    bz4mwf_d.full.BL07830001_0004_0177.pdb    ab4mwf_d.full.BL07830001_0004_0097.pdb    aq4mwf_d.full.BL07830001_0004_0076.pdb    oo4mwf_d.full.BL07830001_0004_0052.pdb    aq4mwf_d.full.BL07830001_0004_0007.pdb    gg4mwf_d.full.BL07830001_0004_0017.pdb    av4mwf_d.full.BL07830001_0004_0040.pdb    bc4mwf_d.full.BL07830001_0004_0079.pdb    ao4mwf_d.full.BL07830001_0004_0110.pdb    ss4mwf_d.full.BL07830001_0004_0021.pdb    an4mwf_d.full.BL07830001_0004_0053.pdb    ai4mwf_d.full.BL07830001_0004_0047.pdb    nn4mwf_d.full.BL07830001_0004_0043.pdb    ak4mwf_d.full.BL07830001_0004_0073.pdb    mm4mwf_d.full.BL07830001_0004_0101.pdb    kk4mwf_d.full.BL07830001_0004_0098.pdb    ap4mwf_d.full.BL07830001_0004_0008.pdb    ll4mwf_d.full.BL07830001_0004_0170.pdb    as4mwf_d.full.BL07830001_0004_0008.pdb    aq4mwf_d.full.BL07830001_0004_0105.pdb    hh4mwf_d.full.BL07830001_0004_0027.pdb    ee4mwf_d.full.BL07830001_0004_0198.pdb    bb4mwf_d.full.BL07830001_0004_0123.pdb    ss4mwf_d.full.BL07830001_0004_0048.pdb    ii4mwf_d.full.BL07830001_0004_0004.pdb    qq4mwf_d.full.BL07830001_0004_0154.pdb    ba4mwf_d.full.BL07830001_0004_0035.pdb    zz4mwf_d.full.BL07830001_0004_0102.pdb    zz4mwf_d.full.BL07830001_0004_0174.pdb    zz4mwf_d.full.BL07830001_0004_0165.pdb    al4mwf_d.full.BL07830001_0004_0169.pdb    bq4mwf_d.full.BL07830001_0004_0083.pdb    bq4mwf_d.full.BL07830001_0004_0022.pdb    ag4mwf_d.full.BL07830001_0004_0169.pdb    yy4mwf_d.full.BL07830001_0004_0101.pdb    ak4mwf_d.full.BL07830001_0004_0079.pdb    bz4mwf_d.full.BL07830001_0004_0167.pdb    ff4mwf_d.full.BL07830001_0004_0196.pdb    bc4mwf_d.full.BL07830001_0004_0069.pdb    hh4mwf_d.full.BL07830001_0004_0038.pdb    hh4mwf_d.full.BL07830001_0004_0118.pdb    ao4mwf_d.full.BL07830001_0004_0139.pdb    qq4mwf_d.full.BL07830001_0004_0189.pdb    nn4mwf_d.full.BL07830001_0004_0109.pdb    pp4mwf_d.full.BL07830001_0004_0179.pdb    ai4mwf_d.full.BL07830001_0004_0193.pdb    ii4mwf_d.full.BL07830001_0004_0093.pdb    ll4mwf_d.full.BL07830001_0004_0155.pdb    ah4mwf_d.full.BL07830001_0004_0193.pdb    as4mwf_d.full.BL07830001_0004_0009.pdb    bd4mwf_d.full.BL07830001_0004_0015.pdb    af4mwf_d.full.BL07830001_0004_0140.pdb    nn4mwf_d.full.BL07830001_0004_0172.pdb    bq4mwf_d.full.BL07830001_0004_0036.pdb    yy4mwf_d.full.BL07830001_0004_0178.pdb    hh4mwf_d.full.BL07830001_0004_0133.pdb    ay4mwf_d.full.BL07830001_0004_0050.pdb    hh4mwf_d.full.BL07830001_0004_0022.pdb    hh4mwf_d.full.BL07830001_0004_0029.pdb    bq4mwf_d.full.BL07830001_0004_0090.pdb    ag4mwf_d.full.BL07830001_0004_0006.pdb    ap4mwf_d.full.BL07830001_0004_0155.pdb    mm4mwf_d.full.BL07830001_0004_0098.pdb    as4mwf_d.full.BL07830001_0004_0199.pdb    ee4mwf_d.full.BL07830001_0004_0094.pdb    kk4mwf_d.full.BL07830001_0004_0169.pdb    ak4mwf_d.full.BL07830001_0004_0057.pdb    bc4mwf_d.full.BL07830001_0004_0130.pdb    an4mwf_d.full.BL07830001_0004_0178.pdb    ac4mwf_d.full.BL07830001_0004_0111.pdb    ii4mwf_d.full.BL07830001_0004_0057.pdb    jj4mwf_d.full.BL07830001_0004_0092.pdb    am4mwf_d.full.BL07830001_0004_0037.pdb    ac4mwf_d.full.BL07830001_0004_0149.pdb    zz4mwf_d.full.BL07830001_0004_0026.pdb    hh4mwf_d.full.BL07830001_0004_0078.pdb    ap4mwf_d.full.BL07830001_0004_0180.pdb    ee4mwf_d.full.BL07830001_0004_0061.pdb    ac4mwf_d.full.BL07830001_0004_0060.pdb    am4mwf_d.full.BL07830001_0004_0173.pdb    az4mwf_d.full.BL07830001_0004_0129.pdb    ll4mwf_d.full.BL07830001_0004_0062.pdb    bd4mwf_d.full.BL07830001_0004_0079.pdb    ac4mwf_d.full.BL07830001_0004_0004.pdb    ll4mwf_d.full.BL07830001_0004_0120.pdb    be4mwf_d.full.BL07830001_0004_0049.pdb    ba4mwf_d.full.BL07830001_0004_0189.pdb    al4mwf_d.full.BL07830001_0004_0008.pdb    ao4mwf_d.full.BL07830001_0004_0024.pdb    pp4mwf_d.full.BL07830001_0004_0164.pdb    ap4mwf_d.full.BL07830001_0004_0169.pdb    ab4mwf_d.full.BL07830001_0004_0179.pdb    ac4mwf_d.full.BL07830001_0004_0040.pdb    qq4mwf_d.full.BL07830001_0004_0153.pdb    av4mwf_d.full.BL07830001_0004_0120.pdb    bb4mwf_d.full.BL07830001_0004_0085.pdb    aq4mwf_d.full.BL07830001_0004_0107.pdb    ee4mwf_d.full.BL07830001_0004_0036.pdb    kk4mwf_d.full.BL07830001_0004_0011.pdb    nn4mwf_d.full.BL07830001_0004_0022.pdb    qq4mwf_d.full.BL07830001_0004_0048.pdb    ag4mwf_d.full.BL07830001_0004_0028.pdb    rr4mwf_d.full.BL07830001_0004_0076.pdb    az4mwf_d.full.BL07830001_0004_0158.pdb    bc4mwf_d.full.BL07830001_0004_0048.pdb    oo4mwf_d.full.BL07830001_0004_0103.pdb    ax4mwf_d.full.BL07830001_0004_0088.pdb    ae4mwf_d.full.BL07830001_0004_0004.pdb    be4mwf_d.full.BL07830001_0004_0072.pdb    mm4mwf_d.full.BL07830001_0004_0084.pdb    pp4mwf_d.full.BL07830001_0004_0171.pdb    mm4mwf_d.full.BL07830001_0004_0107.pdb    pp4mwf_d.full.BL07830001_0004_0115.pdb    ak4mwf_d.full.BL07830001_0004_0160.pdb    ax4mwf_d.full.BL07830001_0004_0108.pdb    af4mwf_d.full.BL07830001_0004_0162.pdb    bb4mwf_d.full.BL07830001_0004_0094.pdb    ak4mwf_d.full.BL07830001_0004_0153.pdb    gg4mwf_d.full.BL07830001_0004_0100.pdb    tt4mwf_d.full.BL07830001_0004_0030.pdb    ag4mwf_d.full.BL07830001_0004_0021.pdb    oo4mwf_d.full.BL07830001_0004_0188.pdb    jj4mwf_d.full.BL07830001_0004_0079.pdb    ap4mwf_d.full.BL07830001_0004_0085.pdb    ah4mwf_d.full.BL07830001_0004_0099.pdb    ae4mwf_d.full.BL07830001_0004_0086.pdb    

ac4mwf_d.full.BL07830001_0004_0067.pdb 86: gg4mwf_d.full.BL07830001_0004_0008.pdb    ag4mwf_d.full.BL07830001_0004_0036.pdb    nn4mwf_d.full.BL07830001_0004_0033.pdb    ai4mwf_d.full.BL07830001_0004_0072.pdb    av4mwf_d.full.BL07830001_0004_0014.pdb    bd4mwf_d.full.BL07830001_0004_0180.pdb    hh4mwf_d.full.BL07830001_0004_0010.pdb    ar4mwf_d.full.BL07830001_0004_0076.pdb    rr4mwf_d.full.BL07830001_0004_0086.pdb    be4mwf_d.full.BL07830001_0004_0035.pdb    jj4mwf_d.full.BL07830001_0004_0086.pdb    rr4mwf_d.full.BL07830001_0004_0077.pdb    kk4mwf_d.full.BL07830001_0004_0166.pdb    am4mwf_d.full.BL07830001_0004_0010.pdb    an4mwf_d.full.BL07830001_0004_0051.pdb    ae4mwf_d.full.BL07830001_0004_0192.pdb    ff4mwf_d.full.BL07830001_0004_0158.pdb    az4mwf_d.full.BL07830001_0004_0110.pdb    ay4mwf_d.full.BL07830001_0004_0038.pdb    ar4mwf_d.full.BL07830001_0004_0008.pdb    ak4mwf_d.full.BL07830001_0004_0189.pdb    ac4mwf_d.full.BL07830001_0004_0123.pdb    qq4mwf_d.full.BL07830001_0004_0133.pdb    yy4mwf_d.full.BL07830001_0004_0156.pdb    av4mwf_d.full.BL07830001_0004_0068.pdb    bv4mwf_d.full.BL07830001_0004_0133.pdb    ll4mwf_d.full.BL07830001_0004_0054.pdb    ae4mwf_d.full.BL07830001_0004_0064.pdb    rr4mwf_d.full.BL07830001_0004_0054.pdb    am4mwf_d.full.BL07830001_0004_0139.pdb    zz4mwf_d.full.BL07830001_0004_0198.pdb    ae4mwf_d.full.BL07830001_0004_0098.pdb    ad4mwf_d.full.BL07830001_0004_0075.pdb    ac4mwf_d.full.BL07830001_0004_0067.pdb    bd4mwf_d.full.BL07830001_0004_0178.pdb    ay4mwf_d.full.BL07830001_0004_0093.pdb    ll4mwf_d.full.BL07830001_0004_0085.pdb    jj4mwf_d.full.BL07830001_0004_0044.pdb    ba4mwf_d.full.BL07830001_0004_0082.pdb    an4mwf_d.full.BL07830001_0004_0137.pdb    tt4mwf_d.full.BL07830001_0004_0018.pdb    yy4mwf_d.full.BL07830001_0004_0161.pdb    ad4mwf_d.full.BL07830001_0004_0017.pdb    ap4mwf_d.full.BL07830001_0004_0031.pdb    bz4mwf_d.full.BL07830001_0004_0135.pdb    zz4mwf_d.full.BL07830001_0004_0022.pdb    be4mwf_d.full.BL07830001_0004_0030.pdb    ad4mwf_d.full.BL07830001_0004_0195.pdb    pp4mwf_d.full.BL07830001_0004_0067.pdb    zz4mwf_d.full.BL07830001_0004_0189.pdb    ay4mwf_d.full.BL07830001_0004_0166.pdb    rr4mwf_d.full.BL07830001_0004_0047.pdb    ab4mwf_d.full.BL07830001_0004_0052.pdb    ah4mwf_d.full.BL07830001_0004_0173.pdb    ax4mwf_d.full.BL07830001_0004_0021.pdb    bc4mwf_d.full.BL07830001_0004_0021.pdb    ll4mwf_d.full.BL07830001_0004_0169.pdb    ll4mwf_d.full.BL07830001_0004_0067.pdb    am4mwf_d.full.BL07830001_0004_0072.pdb    rr4mwf_d.full.BL07830001_0004_0118.pdb    ap4mwf_d.full.BL07830001_0004_0036.pdb    ag4mwf_d.full.BL07830001_0004_0092.pdb    be4mwf_d.full.BL07830001_0004_0189.pdb    qq4mwf_d.full.BL07830001_0004_0110.pdb    bv4mwf_d.full.BL07830001_0004_0129.pdb    ay4mwf_d.full.BL07830001_0004_0146.pdb    ao4mwf_d.full.BL07830001_0004_0144.pdb    aq4mwf_d.full.BL07830001_0004_0165.pdb    mm4mwf_d.full.BL07830001_0004_0021.pdb    ao4mwf_d.full.BL07830001_0004_0147.pdb    bc4mwf_d.full.BL07830001_0004_0119.pdb    be4mwf_d.full.BL07830001_0004_0053.pdb    qq4mwf_d.full.BL07830001_0004_0014.pdb    ac4mwf_d.full.BL07830001_0004_0037.pdb    ac4mwf_d.full.BL07830001_0004_0085.pdb    ar4mwf_d.full.BL07830001_0004_0117.pdb    ss4mwf_d.full.BL07830001_0004_0173.pdb    am4mwf_d.full.BL07830001_0004_0163.pdb    ss4mwf_d.full.BL07830001_0004_0018.pdb    gg4mwf_d.full.BL07830001_0004_0082.pdb    ah4mwf_d.full.BL07830001_0004_0066.pdb    ba4mwf_d.full.BL07830001_0004_0180.pdb    yy4mwf_d.full.BL07830001_0004_0020.pdb    ab4mwf_d.full.BL07830001_0004_0103.pdb    ii4mwf_d.full.BL07830001_0004_0154.pdb    oo4mwf_d.full.BL07830001_0004_0038.pdb    

 

[Anonymous]

In general, calibur gives the information of one single cluster on each line. The information includes the center of the cluster, the size of the cluster, and the members of the cluster.

For instance, the line

ac4mwf_d.full.BL07830001_0004_0067.pdb 86: gg4mwf_d.full.BL07830001_0004_0008.pdb…

first gives the center of the cluster as “ac4mwf_d.full.BL07830001_0004_0067.pdb”, then followed by the size of the cluster, “86”, and finally, a listing of all the 86 decoys in the cluster.

The first line of calibur is the only exception to this rule. It reports the centers of the largest two clusters found, along with their sizes, then finally, the percentage difference between the two sizes. This information is to allow the researcher to decide if the largest cluster is sufficiently larger than the others, in order to consider the next move.

[Anonymous]

Dear kalngyk,

Thank you very much for your answer. What I still dont get is that the numbers dont match up.

In this example, we have the two largest clusters.

One has 304 decoys in and the other 247.

But then the largest is listed in full. Then, the centroid that was previsouly the centriod of the second cluster is now listed as the centroid of the cluster with 174 decoys.

How many clusters do you list in total? Why do the cluster sizes differ?

 

Thank you

L.

[Anonymous]

Calibur shows at most three clusters by default. This can be changed through the -o switch.

The decoy list for each cluster should include the centroid decoy (somewhere in the list).

Each decoy should belong to exactly one cluster. (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-25)

If a decoy appears in more than one list, then there is a bug. If possible, please send us your test case to help us identify the bug.

[Anonymous]

I am not sure it does appear in more clusters. Is just that the number of decoys in that cluster (always the second one, the first one is always the same) appears to have changed.

Can you please look at the my output to see what I mean?

Also, what is the command option for the -o switch? I cannot find that anywhere. I figured out the -c and -r options altough I am still not sure if I can use several residue strechtes for the -r switch (can I use -r 1-30, 68-70?).

Could you please post what all of the options/switches are?

Can you please, please have a look at my question again? I am not sure we are understadning each other.

[Author]

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