List of some PBDs that work and that don't

[neb9]

For reference, the following work (on the July 21 commit, using compress(maskProtein())):

1a7s.pdb  1lt6.pdb  2crt.pdb  3m3r.pdb
1ae5.pdb  1lta.pdb  2dcv.pdb  3m4d.pdb
1ah7.pdb  1ltb.pdb  2dcw.pdb  3m4e.pdb
1am7.pdb  1ltg.pdb  2ddr.pdb  3o44.pdb
1ao6.pdb  1lti.pdb  2dds.pdb  3psm.pdb
1aok.pdb  1lts.pdb  2ddt.pdb  3q76.pdb
1aro.pdb  1ltt.pdb  2dtb.pdb  3q77.pdb
1au8.pdb  1m3i.pdb  2e2f.pdb  3roh.pdb
1ayj.pdb  1m3j.pdb  2ffz.pdb  3sqj.pdb
1b0f.pdb  1md2.pdb  2fgn.pdb  3tdl.pdb
1bah.pdb  1mm0.pdb  2ga4.pdb  3uiv.pdb
1bj5.pdb  1n5u.pdb  2gj0.pdb  3ujo.pdb
1bk8.pdb  1o71.pdb  2gl1.pdb  3ujq.pdb
1bke.pdb  1o72.pdb  2huc.pdb  3uk9.pdb
1bm0.pdb  1o9x.pdb  2i0w.pdb  3ul2.pdb
1bos.pdb  1oba.pdb  2i2z.pdb  3v08.pdb
1brz.pdb  1odb.pdb  2i30.pdb  3vts.pdb
1c01.pdb  1ozz.pdb  2ixu.pdb  3zwg.pdb
1c4q.pdb  1p00.pdb  2ixv.pdb  3zwj.pdb
1ca1.pdb  1p0a.pdb  2j8g.pdb  3zx7.pdb
1cfe.pdb  1p5x.pdb  2k38.pdb  3zxd.pdb
1cgh.pdb  1p6d.pdb  2kam.pdb  3zxg.pdb
1chp.pdb  1p6e.pdb  2kcg.pdb  4dwx.pdb
1chq.pdb  1p9z.pdb  2kgq.pdb  4dyg.pdb
1chv.pdb  1ppf.pdb  2knj.pdb  4fb9.pdb
1cix.pdb  1ppg.pdb  2knm.pdb  4fbb.pdb
1cqf.pdb  1pvl.pdb  2knn.pdb  4fbc.pdb
1cre.pdb  1pzi.pdb  2ks4.pdb  4fbh.pdb
1crf.pdb  1q3j.pdb  2ksg.pdb  4g03.pdb
1ct1.pdb  1qm6.pdb  2kuk.pdb  4g04.pdb
1cxn.pdb  1qmd.pdb  2kyq.pdb  4h56.pdb
1cxo.pdb  1qnu.pdb  2l2b.pdb  4he7.pdb
1cz6.pdb  1qoh.pdb  2l38.pdb  4hgk.pdb
1czg.pdb  1qoy.pdb  2lb7.pdb  4iw2.pdb
1czw.pdb  1r4p.pdb  2lj7.pdb  4iyc.pdb
1d1i.pdb  1r4q.pdb  2lkf.pdb  4iyt.pdb
1d1k.pdb  1rcv.pdb  2lr3.pdb  4izl.pdb
1d9u.pdb  1reo.pdb  2ly5.pdb  4j0o.pdb
1djr.pdb  1rf2.pdb  2ly6.pdb  4jox.pdb
1dkc.pdb  1rgb.pdb  2m8b.pdb  4jta.pdb
1dm0.pdb  1s5b.pdb  2m9g.pdb  4jtc.pdb
1dtc.pdb  1s5c.pdb  2mcw.pdb  4jtd.pdb
1du5.pdb  1s5d.pdb  2mcx.pdb  4k2c.pdb
1e78.pdb  1s5e.pdb  2mp9.pdb  4k71.pdb
1e7a.pdb  1s5f.pdb  2mxz.pdb  4l8u.pdb
1e7b.pdb  1siy.pdb  2mz0.pdb  4l9k.pdb
1e7c.pdb  1t32.pdb  2n0o.pdb  4l9q.pdb
1e7e.pdb  1t5r.pdb  2n2q.pdb  4la0.pdb
1e7f.pdb  1tdk.pdb  2n2r.pdb  4lb2.pdb
1e7g.pdb  1tdn.pdb  2n2z.pdb  4lb9.pdb
1e7h.pdb  1tdo.pdb  2n66.pdb  4m1u.pdb
1e7i.pdb  1tf0.pdb  2n81.pdb  4m3c.pdb
1e8a.pdb  1tgx.pdb  2nrj.pdb  4n0f.pdb
1eef.pdb  1tzq.pdb  2qk7.pdb  4n0u.pdb
1efi.pdb  1ueo.pdb  2rg3.pdb  4oeb.pdb
1fd7.pdb  1ug4.pdb  2uyr.pdb  4om4.pdb
1fgb.pdb  1uor.pdb  2v9u.pdb  4om5.pdb
1fy1.pdb  1ut3.pdb  2vdb.pdb  4or0.pdb
1fy3.pdb  1uun.pdb  2vue.pdb  4p1x.pdb
1g8z.pdb  1xez.pdb  2vuf.pdb  4p1y.pdb
1gni.pdb  1xjt.pdb  2wcd.pdb  4p24.pdb
1gnj.pdb  1xju.pdb  2wcf.pdb  4p2c.pdb
1gps.pdb  1xt3.pdb  2wxt.pdb  4s1y.pdb
1gpt.pdb  1xtc.pdb  2wxu.pdb  4tsy.pdb
1gqm.pdb  1xv3.pdb  2wy6.pdb  4tw1.pdb
1gwy.pdb  1xx1.pdb  2xrq.pdb  4u6v.pdb
1gyg.pdb  1z99.pdb  2xsi.pdb  4ull.pdb
1h09.pdb  1zrv.pdb  2xvq.pdb  4wvm.pdb
1h0j.pdb  1zrw.pdb  2xvu.pdb  4xre.pdb
1h1b.pdb  1zrx.pdb  2xvv.pdb  4yhd.pdb
1h5o.pdb  1zwx.pdb  2xvw.pdb  4z69.pdb
1h9z.pdb  2a9h.pdb  2xw0.pdb  4zgh.pdb
1ha2.pdb  2ap7.pdb  2xw1.pdb  4zpu.pdb
1hk1.pdb  2ap8.pdb  2ydf.pdb  5a09.pdb
1hk2.pdb  2bhi.pdb  2ygt.pdb  5a0a.pdb
1hk3.pdb  2bos.pdb  2ymk.pdb  5a0b.pdb
1hk4.pdb  2brz.pdb  2ymw.pdb  5a0c.pdb
1hk5.pdb  2bx8.pdb  2z7f.pdb  5a8x.pdb
1hne.pdb  2bxa.pdb  3a2e.pdb  5a8y.pdb
1htl.pdb  2bxb.pdb  3a73.pdb  5a8z.pdb
1i02.pdb  2bxc.pdb  3anz.pdb  5aod.pdb
1i2u.pdb  2bxd.pdb  3b07.pdb  5aoe.pdb
1i2v.pdb  2bxe.pdb  3b9l.pdb  5aof.pdb
1iaz.pdb  2bxf.pdb  3b9m.pdb  5dqf.pdb
1iyc.pdb  2bxg.pdb  3bkh.pdb  5ec5.pdb
1jkz.pdb  2bxh.pdb  3bkv.pdb  5fuo.pdb
1jlt.pdb  2bxi.pdb  3chb.pdb  5gaq.pdb
1jqy.pdb  2bxk.pdb  3cx9.pdb  5hoz.pdb
1jr0.pdb  2bxl.pdb  3d3d.pdb  5ifo.pdb
1kbs.pdb  2bxm.pdb  3hc7.pdb  5iih.pdb
1kbt.pdb  2bxn.pdb  3hde.pdb  5iiu.pdb
1kd6.pdb  2bxo.pdb  3i5v.pdb  5iix.pdb
1kho.pdb  2bxp.pdb  3ipv.pdb  5ij5.pdb
1kyn.pdb  2bxq.pdb  3jqz.pdb  5ije.pdb
1lba.pdb  2c5c.pdb  3jry.pdb  5ijf.pdb
1lkf.pdb  2cdx.pdb  3lim.pdb  5k59.pdb
1lt3.pdb  2chb.pdb  3lkf.pdb  7ahl.pdb
1lt4.pdb  2crd.pdb  3lu7.pdb  8tfv.pdb
1lt5.pdb  2crs.pdb  3m2l.pdb

The following do NOT work:

1c48.pdb  3rlg.pdb  4gv5.pdb  4tsp.pdb
1p9g.pdb  3v03.pdb  4i0n.pdb  4tsq.pdb
1rd9.pdb  3v09.pdb  4idj.pdb  4wdc.pdb
1rdp.pdb  3vwi.pdb  4iw1.pdb  4whn.pdb
2anv.pdb  3w9p.pdb  4iya.pdb  4wvp.pdb
2anx.pdb  3weu.pdb  4j0l.pdb  4wx3.pdb
2f9r.pdb  3wev.pdb  4j2v.pdb  4wx5.pdb
2j8f.pdb  3wmu.pdb  4jk4.pdb  4zbq.pdb
2wc8.pdb  3wmv.pdb  4nzl.pdb  4zbr.pdb
2wcb.pdb  4bct.pdb  4ot2.pdb  5abw.pdb
2wce.pdb  4e99.pdb  4pho.pdb  5bpg.pdb
2xrs.pdb  4emx.pdb  4phq.pdb  5cr6.pdb
2xsc.pdb  4f5s.pdb  4po0.pdb  5dby.pdb
3a57.pdb  4f5t.pdb  4q7g.pdb  5elc.pdb
3hdf.pdb  4f5u.pdb  4rw3.pdb  5ele.pdb
3kve.pdb  4f5v.pdb  4rw5.pdb  5elf.pdb
3lu6.pdb  4fba.pdb  4tsl.pdb  5id7.pdb
3lu8.pdb  4fzm.pdb  4tsn.pdb  5id9.pdb
3mxg.pdb  4fzn.pdb  4tso.pdb

Some of this information may be useful for tests & debugging.

[graik]

All trouble-makers tested in DSSP.py TestLong and, with the new output parsing, there is no problem any longer.