[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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