    data/concavity-0.1+dfsg.1/apps/concavity/concavity.C:727: theshold ==> threshold
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:165: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:166: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:167: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:168: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:169: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:170: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:241: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:242: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:243: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:244: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:245: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:246: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:297: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:298: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:299: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:300: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:301: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:302: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1048: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1049: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1050: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1051: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1052: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1305: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1306: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1307: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1308: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1309: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1392: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1393: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1394: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1395: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1396: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1562: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1563: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1564: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1565: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1566: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1567: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1584: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1585: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1586: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1587: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1588: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1589: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1603: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1604: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1605: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1606: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1607: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1608: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1656: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1657: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1658: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1659: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1660: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1661: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1860: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1861: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1862: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1863: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1864: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1865: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1936: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1937: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1938: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1939: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1940: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1941: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1992: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1993: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1994: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1995: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1996: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:1997: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:2741: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:2742: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:2743: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:2744: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:2745: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:2746: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:2997: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:2998: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:2999: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3000: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3001: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3084: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3085: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3086: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3087: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3088: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3089: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3253: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3254: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3255: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3256: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3257: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3258: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3275: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3276: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3277: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3278: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3279: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3280: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3294: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3295: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3296: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3297: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3298: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3348: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3349: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3350: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3351: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3352: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3562: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3563: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3564: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3565: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3566: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3567: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3638: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3639: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3640: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3641: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3642: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3643: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3694: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3695: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3696: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3697: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3698: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:3699: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4443: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4444: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4445: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4446: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4447: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4448: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4699: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4700: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4701: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4702: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4703: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4786: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4787: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4788: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4789: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4790: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4791: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4955: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4956: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4957: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4958: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4959: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4960: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4977: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4978: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4979: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4980: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4981: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4982: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4996: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4997: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4998: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:4999: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5000: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5050: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5051: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5052: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5053: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5054: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5278: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5279: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5280: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5281: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5282: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5283: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5354: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5355: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5356: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5357: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5358: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5359: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5410: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5411: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5412: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5413: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5414: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:5415: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6161: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6162: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6163: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6164: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6165: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6418: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6419: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6420: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6421: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6422: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6505: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6506: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6507: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6508: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6509: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6675: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6676: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6677: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6678: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6679: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6680: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6697: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6698: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6699: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6700: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6701: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6702: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6716: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6717: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6718: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6719: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6720: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6721: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6769: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6770: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6771: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6772: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6773: SER ==> SET
    data/concavity-0.1+dfsg.1/examples/1G6C.pdb:6774: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/PDBResidue.C:456: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/PDBAminoAcid.C:34: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/charm22.txt:244: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/charm22.txt:245: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/charm22.txt:246: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/charm22.txt:247: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/charm22.txt:248: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/charm22.txt:249: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/charm22.txt:250: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/charm22.txt:251: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/charm22.txt:252: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/charm22.txt:253: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/charm22.txt:254: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/amino_acid_atoms.txt:137: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/amino_acid_atoms.txt:138: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/amino_acid_atoms.txt:139: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/amino_acid_atoms.txt:140: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/amino_acid_atoms.txt:141: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/amino_acid_atoms.txt:142: SER ==> SET
    data/concavity-0.1+dfsg.1/pkgs/PDB/PDBAtomTypes.h:348: Ser ==> Set
    data/concavity-0.1+dfsg.1/pkgs/PDB/PDBUtil.C:487: canoncial ==> canonical
    data/concavity-0.1+dfsg.1/pkgs/PDB/PDBUtil.C:497: canoncial ==> canonical
    data/concavity-0.1+dfsg.1/pkgs/PDB/PDBUtil.C:507: canoncial ==> canonical
    data/concavity-0.1+dfsg.1/pkgs/R2Shapes/R2Grid.C:1100: Initalize ==> Initialize
    data/concavity-0.1+dfsg.1/pkgs/R2Shapes/R2Grid.C:1787: initalize ==> initialize
    data/concavity-0.1+dfsg.1/pkgs/R2Shapes/R2Grid.C:2161: outputing ==> outputting
    data/concavity-0.1+dfsg.1/pkgs/R3Shapes/R3MeshSearchTree.C.sav:969: decendents ==> descendents, descendants
    data/concavity-0.1+dfsg.1/pkgs/R3Shapes/R3Cylinder.h:22: propetry ==> property
    data/concavity-0.1+dfsg.1/pkgs/R3Shapes/R3Cylinder.h:31: propetry ==> property
    data/concavity-0.1+dfsg.1/pkgs/R3Shapes/R3Cone.h:22: propetry ==> property
    data/concavity-0.1+dfsg.1/pkgs/R3Shapes/R3Cone.h:31: propetry ==> property
    data/concavity-0.1+dfsg.1/pkgs/R3Shapes/R3Kdtree.C:613: decendents ==> descendents, descendants
    data/concavity-0.1+dfsg.1/pkgs/R3Shapes/R3MeshSearchTree.C:1019: decendents ==> descendents, descendants
    data/concavity-0.1+dfsg.1/pkgs/R3Shapes/R3Draw.C:327: Ammend ==> Amend
    data/concavity-0.1+dfsg.1/pkgs/R3Shapes/R4Matrix.C:10: hierachy ==> hierarchy
    data/concavity-0.1+dfsg.1/pkgs/R3Shapes/R3Grid.C:925: Initalize ==> Initialize
    data/concavity-0.1+dfsg.1/pkgs/R3Shapes/R3Grid.C:1116: Initalize ==> Initialize
    data/concavity-0.1+dfsg.1/pkgs/R3Shapes/R3Mesh.C:2983: filname ==> filename
    data/concavity-0.1+dfsg.1/pkgs/R3Shapes/R3Mesh.h:81: interesection ==> intersection
    data/concavity-0.1+dfsg.1/pkgs/RNBasics/RNBasics.h:8: Compatability ==> Compatibility
    data/concavity-0.1+dfsg.1/pkgs/RNBasics/RNSvd.C:134: contruct ==> construct
    data/concavity-0.1+dfsg.1/pkgs/RNBasics/RNSvd.C:432: loger ==> logger, lodger, longer
    data/concavity-0.1+dfsg.1/pkgs/RNBasics/RNSvd.C:475: propogate ==> propagate
    data/concavity-0.1+dfsg.1/pkgs/RNBasics/RNCompat.h:78: Compatability ==> Compatibility
    data/concavity-0.1+dfsg.1/pkgs/R3Graphics/R3PointLight.h:69: threshhold ==> threshold
    data/concavity-0.1+dfsg.1/debian/patches/spelling:11: treshold ==> threshold
    data/concavity-0.1+dfsg.1/.pc/spelling/apps/concavity/pocket_extraction.C:1031: treshold ==> threshold
    data/concavity-0.1+dfsg.1/.pc/noopengllink/pkgs/RNBasics/RNCompat.h:81: Compatability ==> Compatibility
    data/concavity-0.1+dfsg.1/.pc/noopengllink/pkgs/R3Shapes/R3Mesh.C:3245: filname ==> filename
    data/concavity-0.1+dfsg.1/.pc/noopengllink/pkgs/R3Shapes/R3Mesh.h:81: interesection ==> intersection
    data/concavity-0.1+dfsg.1/.pc/noopengllink/pkgs/R3Shapes/R3Grid.C:925: Initalize ==> Initialize
    data/concavity-0.1+dfsg.1/.pc/noopengllink/pkgs/R3Shapes/R3Grid.C:1116: Initalize ==> Initialize
    data/concavity-0.1+dfsg.1/.pc/noopengllink/pkgs/R2Shapes/R2Grid.C:1100: Initalize ==> Initialize
    data/concavity-0.1+dfsg.1/.pc/noopengllink/pkgs/R2Shapes/R2Grid.C:1785: initalize ==> initialize
    data/concavity-0.1+dfsg.1/.pc/noopengllink/pkgs/R2Shapes/R2Grid.C:2159: outputing ==> outputting
    data/concavity-0.1+dfsg.1/.pc/compiler_errors/pkgs/PDB/PDBUtil.C:487: canoncial ==> canonical
    data/concavity-0.1+dfsg.1/.pc/compiler_errors/pkgs/PDB/PDBUtil.C:497: canoncial ==> canonical
    data/concavity-0.1+dfsg.1/.pc/compiler_errors/pkgs/PDB/PDBUtil.C:507: canoncial ==> canonical
    data/concavity-0.1+dfsg.1/.pc/compiler_errors/pkgs/R3Shapes/R3Grid.C:925: Initalize ==> Initialize
    data/concavity-0.1+dfsg.1/.pc/compiler_errors/pkgs/R3Shapes/R3Grid.C:1116: Initalize ==> Initialize
    data/concavity-0.1+dfsg.1/.pc/threshold_range_cutoff/apps/concavity/concavity.C:723: theshold ==> threshold
    data/concavity-0.1+dfsg.1/.pc/remove_ply/pkgs/R3Shapes/R3Mesh.C:3246: filname ==> filename
    data/concavity-0.1+dfsg.1/.pc/remove_ply/pkgs/R3Shapes/R3Mesh.h:81: interesection ==> intersection