[Bioperl-l] RE: about pdb parsing
Jurgen Pletinckx
jurgen.pletinckx at algonomics.com
Tue Nov 18 06:22:16 EST 2003
# In attachment, you can find a sample script together with
# sample output.
And, as usual, the actual attachments come later. Sorry
about that.
--
Jurgen Pletinckx
AlgoNomics NV
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pdb1sw6.ent 1SW6 A 253 GLY-212 GLY-512
pdb1sw6.ent 1SW6 B 253 GLY-212 GLY-512
pdb1sw6.ent 1SW6 default 214 HOH-1 HOH-216
pdb1swa.ent 1SWA A 119 GLY-16 PRO-135
pdb1swa.ent 1SWA B 114 GLY-16 VAL-133
pdb1swa.ent 1SWA C 114 GLY-16 VAL-133
pdb1swa.ent 1SWA D 114 GLY-16 VAL-133
pdb1swa.ent 1SWA default 210 HOH-201 HOH-411
pdb1swb.ent 1SWB A 119 GLY-16 PRO-135
pdb1swb.ent 1SWB B 114 GLY-16 VAL-133
pdb1swb.ent 1SWB C 114 GLY-16 VAL-133
pdb1swb.ent 1SWB D 114 GLY-16 VAL-133
pdb1swb.ent 1SWB default 208 HOH-201 HOH-409
pdb1swc.ent 1SWC A 113 GLY-16 LYS-132
pdb1swc.ent 1SWC B 116 GLY-16 LYS-132
pdb1swc.ent 1SWC C 112 GLY-16 LYS-132
pdb1swc.ent 1SWC D 116 GLY-16 LYS-132
pdb1swc.ent 1SWC default 225 HOH-201 HOH-426
pdb1swd.ent 1SWD A 116 GLY-16 LYS-132
pdb1swd.ent 1SWD B 113 GLY-16 VAL-133
pdb1swd.ent 1SWD C 114 GLY-16 VAL-133
pdb1swd.ent 1SWD D 117 GLY-16 VAL-133
pdb1swd.ent 1SWD default 235 BTN-300 HOH-434
pdb1swe.ent 1SWE A 116 GLY-16 LYS-132
pdb1swe.ent 1SWE B 117 GLY-16 VAL-133
pdb1swe.ent 1SWE C 117 GLY-16 VAL-133
pdb1swe.ent 1SWE D 117 GLY-16 VAL-133
pdb1swe.ent 1SWE default 305 BTN-300 HOH-502
pdb1swf.ent 1SWF A 115 SER-52 SER-45
pdb1swf.ent 1SWF B 124 SER-52 SER-45
pdb1swf.ent 1SWF C 124 SER-52 SER-45
pdb1swf.ent 1SWF D 115 SER-52 SER-45
pdb1swf.ent 1SWF default 213 HOH-201 HOH-414
pdb1swg.ent 1SWG A 111 SER-52 ALA-46
pdb1swg.ent 1SWG B 111 SER-52 ALA-46
pdb1swg.ent 1SWG C 125 SER-52 ALA-46
pdb1swg.ent 1SWG D 112 GLU-51 SER-45
pdb1swg.ent 1SWG default 338 BTN-600 HOH-535
pdb1swh.ent 1SWH A 113 GLY-16 PRO-135
pdb1swh.ent 1SWH B 114 GLY-16 VAL-133
pdb1swh.ent 1SWH C 114 GLY-16 VAL-133
pdb1swh.ent 1SWH D 114 GLY-16 VAL-133
pdb1swh.ent 1SWH default 198 HOH-201 HOH-399
pdb1swi.ent 1SWI A 30 ARG-1 GLY-31
pdb1swi.ent 1SWI B 29 ARG-1 VAL-30
pdb1swi.ent 1SWI C 29 ARG-1 VAL-30
pdb1swi.ent 1SWI default 29 BNZ-100 HOH-78
pdb1swj.ent 1SWJ A 111 GLY-16 LYS-132
pdb1swj.ent 1SWJ B 117 GLY-16 VAL-133
pdb1swj.ent 1SWJ C 116 GLY-16 LYS-132
pdb1swj.ent 1SWJ D 112 GLY-16 VAL-133
pdb1swj.ent 1SWJ default 206 HOH-201 HOH-407
pdb1swk.ent 1SWK A 116 GLY-16 LYS-132
pdb1swk.ent 1SWK B 116 GLY-16 LYS-132
pdb1swk.ent 1SWK C 116 GLY-16 LYS-132
pdb1swk.ent 1SWK D 116 GLY-16 LYS-132
pdb1swk.ent 1SWK default 214 BTN-5100 HOH-6211
pdb1swl.ent 1SWL A 118 GLY-16 LYS-134
pdb1swl.ent 1SWL B 113 GLY-16 VAL-133
pdb1swl.ent 1SWL C 110 GLY-16 VAL-133
pdb1swl.ent 1SWL D 110 GLY-16 VAL-133
pdb1swl.ent 1SWL default 176 HOH-201 HOH-377
pdb1swm.ent 1SWM default 278 VAL-1 HOH-123
pdb1swn.ent 1SWN A 119 GLY-16 PRO-135
pdb1swn.ent 1SWN B 113 GLY-16 VAL-133
pdb1swn.ent 1SWN C 117 GLY-16 VAL-133
pdb1swn.ent 1SWN D 117 GLY-16 VAL-133
pdb1swn.ent 1SWN default 194 BTN-300 HOH-392
pdb1swo.ent 1SWO A 119 GLY-16 PRO-135
pdb1swo.ent 1SWO B 114 GLY-16 VAL-133
pdb1swo.ent 1SWO C 114 GLY-16 VAL-133
pdb1swo.ent 1SWO D 114 GLY-16 VAL-133
pdb1swo.ent 1SWO default 227 HOH-201 HOH-6228
pdb1swp.ent 1SWP A 116 GLY-16 LYS-132
pdb1swp.ent 1SWP B 116 GLY-16 LYS-132
pdb1swp.ent 1SWP C 116 GLY-16 LYS-132
pdb1swp.ent 1SWP D 116 GLY-16 LYS-132
pdb1swp.ent 1SWP default 188 BTN-300 HOH-385
pdb1swq.ent 1SWQ A 112 GLY-16 PRO-135
pdb1swq.ent 1SWQ B 113 GLY-16 VAL-133
pdb1swq.ent 1SWQ C 111 GLY-16 VAL-133
pdb1swq.ent 1SWQ D 113 GLY-16 VAL-133
pdb1swq.ent 1SWQ default 239 HOH-201 HOH-440
pdb1swr.ent 1SWR A 116 GLY-16 LYS-132
pdb1swr.ent 1SWR B 117 GLY-16 VAL-133
pdb1swr.ent 1SWR C 117 GLY-16 VAL-133
pdb1swr.ent 1SWR D 117 GLY-16 VAL-133
pdb1swr.ent 1SWR default 210 BTN-300 HOH-407
pdb1sws.ent 1SWS A 113 GLY-16 LYS-132
pdb1sws.ent 1SWS B 116 GLY-16 LYS-132
pdb1sws.ent 1SWS C 112 GLY-16 LYS-132
pdb1sws.ent 1SWS D 111 GLY-16 LYS-132
pdb1sws.ent 1SWS default 177 HOH-201 HOH-378
pdb1swt.ent 1SWT A 117 GLY-16 VAL-133
pdb1swt.ent 1SWT B 116 GLY-16 LYS-132
pdb1swt.ent 1SWT default 105 BTN-500 HOH-304
Exception found for input /xlv1/db/pdb/uncompressed_files/sw/pdb1swu.ent
------------- EXCEPTION -------------
MSG: A ANISOU record should have the same O0 as the previous record O2
STACK Bio::Structure::IO::pdb::_read_PDB_coordinate_section /usr/local/lib/perl5/site_perl/5.6.1/Bio/Structure/IO/pdb.pm:1277
STACK Bio::Structure::IO::pdb::next_structure /usr/local/lib/perl5/site_perl/5.6.1/Bio/Structure/IO/pdb.pm:459
STACK (eval) read.pl:16
STACK toplevel read.pl:13
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