Hi, On Thu, Jun 16, 2011 at 7:49 AM, Jan Dohnalek <dohnalek...@gmail.com> wrote:
> > Modeling more UNKNOWN atoms might be the future for these cases? > one needs to specify chemical element type in 77-78 position, otherwise these records are useless. Example: http://www.rcsb.org/pdb/files/3GR4.pdb HETATM15389 UNK UNX A 532 -18.118 17.844 4.079 0.01 2.00 X HETATM15390 UNK UNX A 533 -8.272 -3.498 -6.221 0.01 2.00 X HETATM15391 UNK UNX A 534 -25.115 16.818 6.611 0.01 2.00 X HETATM15392 UNK UNX A 535 -6.573 1.578 13.603 0.01 2.00 X HETATM15393 UNK UNX A 536 -33.370 1.951 -7.370 0.01 2.00 X HETATM15394 UNK UNX A 537 -10.543 13.880 25.677 0.01 2.00 X or another one: http://www.rcsb.org/pdb/files/1au9.pdb HETATM 1951 UNK UNX A 277 -4.504 49.776 37.073 1.00 16.17 X HETATM 1952 UNK UNX A 278 -4.010 50.094 38.754 0.25 15.17 X I'm puzzled about how occupancy and B were defined? There is no element X, so these "atoms" can't be used in Fcalc calculation. There quite a few of them in PDB (see below). Pavel. 1au9.log: "HETATM 1951 UNK UNX A 277 .*. X " 1b3o.log: "HETATM 5493 UNK UNX B 632 .*. X " 1h1a.log: "HETATM 3018 UNK UNX A1193 .*. X " 1i1w.log: "HETATM 4554 UNK UNX A1406 .*. X " 1itk.log: "HETATM11213 UNK UNX A2017 .*. X " 1j5e.log: "HETATM51767 UNK UNX A1545 .*. X " 1ji4.log: "HETATM14366 UNK UNX A 802 .*. X " 1kdg.log: "HETATM 8430 UNK UNX B 904 .*. X " 1lfo.log: "HETATM 1052 UNK UNX A 131 .*. X " 1obp.log: "HETATM 3161 UNK UNX A 161 .*. X " 1r9l.log: "HETATM 2391 UNK UNX A1310 .*. X " 1r9q.log: "HETATM 2383 UNK UNX A1310 .*. X " 1rkt.log: "HETATM 3389 UNK UNX A 415 .*. X " 1s3l.log: "HETATM 2662 UNK UNX A 503 .*. X " 1s9r.log: "HETATM 6562 UNK UNX A 956 .*. X " 1som.log: "HETATM 4204 UNK UNX A1000 .*. X " 1xho.log: "HETATM 2573 UNK UNX B 119 .*. X " 1xi3.log: "HETATM 3057 UNK UNX A 403 .*. X " 1xma.log: "HETATM 1723 UNK UNX A 403 .*. X " 1xqu.log: "HETATM 1736 UNK UNX A 401 .*. X " 1xrg.log: "HETATM 3035 UNK UNX A 401 .*. X " 1xx7.log: "HETATM 7736 UNK UNX A2001 .*. X " 1y80.log: "HETATM 1012 UNK UNX A 601 .*. X " 1y81.log: "HETATM 939 UNK UNX A 401 .*. X " 1y82.log: "HETATM 4478 UNK UNX A 303 .*. X " 1yb3.log: "HETATM 1425 UNK UNX A 401 .*. X " 1ybx.log: "HETATM 1348 UNK UNX A 201 .*. X " 1yby.log: "HETATM 2729 UNK UNX A1004 .*. X " 1ybz.log: "HETATM 602 UNK UNX A 101 .*. X " 1yd7.log: "HETATM 1281 UNK UNX A 388 .*. X " 1yem.log: "HETATM 2700 UNK UNX A 202 .*. X " 1z2u.log: "HETATM 1288 UNK UNX A 501 .*. X " 1zd0.log: "HETATM 1142 UNK UNX A 401 .*. X " 1zgh.log: "HETATM 1811 UNK UNX A 231 .*. X " 1zuu.log: "HETATM 538 UNK UNX A1001 .*. X " 2a4k.log: "HETATM 3122 UNK UNX A 264 .*. X " 2aed.log: "HETATM 1217 UNK UNX A 301 .*. X " 2ajp.log: "HETATM 4594 UNK UNX A 402 .*. X " 2amx.log: "HETATM 5871 UNK UNX A2000 .*. X " 2ar0.log: "HETATM 7678 UNK UNX A1001 .*. X " 2awp.log: "HETATM 3181 UNK UNX A1000 .*. X " 2ayv.log: "HETATM 1140 UNK UNX A 147 .*. X " 2b0r.log: "HETATM 2435 UNK UNX A1001 .*. X " 2b25.log: "HETATM 3834 UNK UNX A 701 .*. X " 2b6h.log: "HETATM 1388 UNK UNX A 301 .*. X " 2c4b.log: "HETATM 2536 UNK UNX D 1 .*. X " 2chh.log: "HETATM 934 UNK UNX A1116 .*. X " 2dyr.log: "HETATM28937 UNK UNX C 262 .*. X " 2dys.log: "HETATM28967 UNK UNX C 262 .*. X " 2f4z.log: "HETATM 2268 UNK UNX B4000 .*. X " 2fol.log: "HETATM 1271 UNK UNX A 401 .*. X " 2fv7.log: "HETATM 4571 UNK UNX A 501 .*. X " 2gao.log: "HETATM 2692 UNK UNX A 602 .*. X " 2h16.log: "HETATM 4869 UNK UNX A2001 .*. X " 2h17.log: "HETATM 1344 UNK UNX A 301 .*. X " 2h18.log: "HETATM 1419 UNK UNX A 401 .*. X " 2h57.log: "HETATM 3955 UNK UNX A 503 .*. X " 2h58.log: "HETATM 2552 UNK UNX A 401 .*. X " 2heh.log: "HETATM 2523 UNK UNX A 801 .*. X " 2hlz.log: "HETATM 9050 UNK UNX A 701 .*. X " 2hp0.log: "HETATM 6991 UNK UNX A1101 .*. X " 2hp3.log: "HETATM 6895 UNK UNX A1201 .*. X " 2hte.log: "HETATM 6731 UNK UNX A3002 .*. X " 2hup.log: "HETATM 2487 UNK UNX A 401 .*. X " 2i7q.log: "HETATM 2855 UNK UNX A1001 .*. X " 2ig7.log: "HETATM 5622 UNK UNX A1004 .*. X " 2ija.log: "HETATM 2434 UNK UNX A 501 .*. X " 2il1.log: "HETATM 1326 UNK UNX A1401 .*. X " 2iqj.log: "HETATM 1949 UNK UNX A1001 .*. X " 2jax.log: "HETATM 2008 UNK UNX A1297 .*. X " 2jbv.log: "HETATM 8225 UNK UNX A2500 .*. X " 2jcm.log: "HETATM 3839 UNK UNX A1489 .*. X " 2jim.log: "HETATM 5752 UNK UNX A 813 .*. X " 2jio.log: "HETATM 5771 UNK UNX A 813 .*. X " 2jip.log: "HETATM 5727 UNK UNX A 813 .*. X " 2jiq.log: "HETATM 5727 UNK UNX A 813 .*. X " 2nzt.log: "HETATM13368 UNK UNX A 1 .*. X " 2o1z.log: "HETATM 4415 UNK UNX A2001 .*. X " 2o52.log: "HETATM 2572 UNK UNX A1003 .*. X " 2ocb.log: "HETATM 1403 UNK UNX A1001 .*. X " 2oil.log: "HETATM 1367 UNK UNX A1001 .*. X " 2olm.log: "HETATM 1092 UNK UNX A1001 .*. X " 2p57.log: "HETATM 984 UNK UNX A 202 .*. X " 2p5s.log: "HETATM 2461 UNK UNX A 101 .*. X " 2pfr.log: "HETATM 4716 UNK UNX A1002 .*. X " 2pmu.log: "HETATM 4832 UNK UNX A6002 .*. X " 2pq8.log: "HETATM 2174 UNK UNX A 701 .*. X " 2pqt.log: "HETATM 2400 UNK UNX A 401 .*. X " 2px4.log: "HETATM 2114 UNK UNX A 801 .*. X " 2qsy.log: "HETATM 1510 UNK UNX A1103 .*. X " 2qsz.log: "HETATM 1589 UNK UNX A1001 .*. X " 2qt1.log: "HETATM 1612 UNK UNX A 203 .*. X " 2r2q.log: "HETATM 1908 UNK UNX A 1 .*. X " 2r8t.log: "HETATM 2409 UNK UNX A 338 .*. X " 2rep.log: "HETATM 2183 UNK UNX A 1 .*. X " 2rex.log: "HETATM 4296 UNK UNX A 1 .*. X " 2v3v.log: "HETATM 5782 UNK UNX A 813 .*. X " 2v45.log: "HETATM 5752 UNK UNX A 813 .*. X " 2vya.log: "HETATM 8368 UNK UNX A1576 .*. X " 2w2j.log: "HETATM 2289 UNK UNX A 601 .*. X " 2wbi.log: "HETATM 6139 UNK UNX A1428 .*. X " 2wtl.log: "HETATM 7799 UNK UNX A1001 .*. X " 2x2u.log: "HETATM 1955 UNK UNX A1283 .*. X " 2x8b.log: "HETATM 4669 UNK UNX A1556 .*. X " 2zxw.log: "HETATM28739 UNK UNX C 262 .*. X " 3a1p.log: "HETATM 3915 UNK UNX D 500 .*. X " 3abk.log: "HETATM28972 UNK UNX C 262 .*. X " 3abl.log: "HETATM28739 UNK UNX C 262 .*. X " 3abm.log: "HETATM28654 UNK UNX C 262 .*. X " 3ag1.log: "HETATM28969 UNK UNX C 262 .*. X " 3ag2.log: "HETATM28998 UNK UNX C 262 .*. X " 3ag3.log: "HETATM28921 UNK UNX C 262 .*. X " 3ag4.log: "HETATM28854 UNK UNX C 262 .*. X " 3b6u.log: "HETATM 5169 UNK UNX A 403 .*. X " 3b6v.log: "HETATM 4537 UNK UNX A1003 .*. X " 3bfn.log: "HETATM 2194 UNK UNX A 701 .*. X " 3big.log: "HETATM 2430 UNK UNX A 400 .*. X " 3bih.log: "HETATM 2405 UNK UNX A 400 .*. X " 3c5c.log: "HETATM 5222 UNK UNX A 204 .*. X " 3c6g.log: "HETATM 7630 UNK UNX A 1 .*. X " 3cbq.log: "HETATM 1348 UNK UNX A 1 .*. X " 3chb.log: "HETATM 4161 UNK UNX D 109 .*. X " 3con.log: "HETATM 1250 UNK UNX A 206 .*. X " 3cpf.log: "HETATM 1892 UNK UNX A 1 .*. X " 3cxl.log: "HETATM 3171 UNK UNX A 503 .*. X " 3czh.log: "HETATM 7639 UNK UNX A 1 .*. X " 3dax.log: "HETATM 7565 UNK UNX A 1 .*. X " 3day.log: "HETATM 4287 UNK UNX A 681 .*. X " 3dlj.log: "HETATM 7188 UNK UNX A2004 .*. X " 3dwd.log: "HETATM 1761 UNK UNX A 502 .*. X " 3dz8.log: "HETATM 1428 UNK UNX A 501 .*. X " 3dzx.log: "HETATM 2238 UNK UNX A 1 .*. X " 3e43.log: "HETATM 4435 UNK UNX A 259 .*. X " 3eap.log: "HETATM 6466 UNK UNX A 254 .*. X " 3edt.log: "HETATM 8082 UNK UNX D 1 .*. X " 3eo2.log: "HETATM 1470 UNK UNX A 1 .*. X " 3f2r.log: "HETATM 5368 UNK UNX A 606 .*. X " 3feg.log: "HETATM 2998 UNK UNX A 400 .*. X " 3feh.log: "HETATM 2860 UNK UNX A 501 .*. X " 3fk2.log: "HETATM 6162 UNK UNX A 1 .*. X " 3flv.log: "HETATM 1516 UNK UNX B 102 .*. X " 3fm8.log: "HETATM 7167 UNK UNX A 6 .*. X " 3fye.log: "HETATM12580 UNK UNX A 573 .*. X " 3fzy.log: "HETATM 3524 UNK UNX A 323 .*. X " 3g15.log: "HETATM 5455 UNK UNX A 606 .*. X " 3g2g.log: "HETATM14619 UNK UNX A 534 .*. X " 3gf9.log: "HETATM 1411 UNK UNX A 1 .*. X " 3gft.log: "HETATM 7772 UNK UNX A 170 .*. X " 3gqy.log: "HETATM15091 UNK UNX A 532 .*. X " 3gr4.log: "HETATM15389 UNK UNX A 532 .*. X " 3gro.log: "HETATM 4238 UNK UNX A 3 .*. X " 3h5z.log: "HETATM 3482 UNK UNX A3001 .*. X " 3h6n.log: "HETATM 779 UNK UNX A1679 .*. X " 3h6o.log: "HETATM14786 UNK UNX A 532 .*. X " 3hlj.log: "HETATM 2100 UNK UNX A 264 .*. X " 3hm6.log: "HETATM 4081 UNK UNX X 1 .*. X " 3i44.log: "HETATM 3649 UNK UNX A 478 .*. X " 3ihw.log: "HETATM 1299 UNK UNX A 1 .*. X " 3ijp.log: "HETATM 4064 UNK UNX A 268 .*. X " 3inn.log: "HETATM 8683 UNK UNX A 301 .*. X " 3iug.log: "HETATM 2998 UNK UNX A 6 .*. X " 3jzy.log: "HETATM 1080 UNK UNX A 1 .*. X " 3k35.log: "HETATM12819 UNK UNX A 322 .*. X " 3k5k.log: "HETATM 4292 UNK UNX A1199 .*. X " 3krb.log: "HETATM 4959 UNK UNX A 402 .*. X " 3krs.log: "HETATM 3917 UNK UNX A 302 .*. X " 3kup.log: "HETATM 1843 UNK UNX A 3 .*. X " 3kuq.log: "HETATM 1510 UNK UNX A 1 .*. X " 3kuz.log: "HETATM 1611 UNK UNX A 1 .*. X " 3kxa.log: "HETATM 4108 UNK UNX A 201 .*. X " 3l46.log: "HETATM 1497 UNK UNX A 3 .*. X " 3l4b.log: "HETATM 9053 UNK UNX B 145 .*. X " 3lgd.log: "HETATM 7908 UNK UNX A 951 .*. X " 3llu.log: "HETATM 1551 UNK UNX A 1 .*. X " 3lp8.log: "HETATM 3195 UNK UNX A 423 .*. X " 3lq3.log: "HETATM 2900 UNK UNX A 398 .*. X " 3lx7.log: "HETATM 1129 UNK UNX A 294 .*. X " 3lxw.log: "HETATM 3137 UNK UNX A 1 .*. X " 3md0.log: "HETATM 2244 UNK UNX A 336 .*. X " 3me3.log: "HETATM15227 UNK UNX A 533 .*. X " 3met.log: "HETATM 2873 UNK UNX A 1 .*. X " 3nni.log: "HETATM 4124 UNK UNX A 4 .*. X " 3nwn.log: "HETATM 2456 UNK UNX A1001 .*. X " 4hb1.log: "HETATM 362 UNK UNX A 801 .*. X " 4uag.log: "HETATM 3299 UNK UNX A 986 .*. X "
