Methods
Using the methods sql, metallopdb and rssmetallopdb

Excercizing the sql method

[query: 'select source_id,description from protein limit 3']
source_id: 1aoo
description: Header: [metallothionein 08-jul-97 1aoo] Title: [ag-substituted metallothionein from saccharomyces cerevisiae, nmr, minimized average structure] Compound: [mol_id: 1; molecule: ag-metallothionein; chain: null; synonym: ag-mt; biological_unit: monomer; other_details: ag(i) substituted] Source: [mol_id: 1; organism_scientific: saccharomyces cerevisiae; organism_common: baker's yeast; strain: 301n] Keywords: [copper detoxification, metal-thiolate cluster]
0:
source_id: 1aqq
description: Header: [metallothionein 31-jul-97 1aqq] Title: [ag-substituted metallothionein from saccharomyces cerevisiae, nmr, 10 structures] Compound: [mol_id: 1; molecule: ag-metallothionein; chain: null; synonym: ag-mt; biological_unit: monomer; other_details: ag(i) substituted] Source: [mol_id: 1; organism_scientific: saccharomyces cerevisiae; organism_common: baker's yeast; strain: 301n] Keywords: [copper detoxification, metal-thiolate cluster]
1:
source_id: 2aw0
description: Header: [copper transport 08-oct-97 2aw0] Title: [fourth metal-binding domain of the menkes copper-transporting atpase, nmr, 20 structures] Compound: [mol_id: 1; molecule: menkes copper-transporting atpase; chain: null; fragment: fourth metal-binding domain; ec: 3.6.1.36; engineered: yes; biological_unit: monomer; other_details: ag(i)-bound state] Source: [mol_id: 1; organism_scientific: homo sapiens; organism_common: human; expression_system: escherichia coli] Keywords: [copper-binding domain, hydrolase, copper transport]
2:

Making a deliberate error using the metallopdb method

[metal: zn][mode: first][count: -3]
OOPS we got an error
error_message_prefix: PHP
mode: 1
level: 1024
code: SOAP-ENV:Server
message: Parameter count must be an integer > 0, value sent: -3
userinfo: Errno: 256 Filename: /export/asd/metallo2/metallodb/webdocs/services/soap.php Lineno: 46
file: /home/server/php/lib/php/SOAP/Fault.php
line: 49
function: pear_error
class: pear_error
type: ::
0: Parameter count must be an integer > 0, value sent: -3
1: SOAP-ENV:Server
2:
3:
4: Errno: 256 Filename: /export/asd/metallo2/metallodb/webdocs/services/soap.php Lineno: 46
args:
0:
file: /home/server/php/lib/php/SOAP/Base.php
line: 320
function: soap_fault
class: soap_fault
type: ->
0: Parameter count must be an integer > 0, value sent: -3
1: SOAP-ENV:Server
2: PHP
3: Errno: 256 Filename: /export/asd/metallo2/metallodb/webdocs/services/soap.php Lineno: 46
4:
5:
args:
1:
file: /home/server/php/lib/php/SOAP/Client.php
line: 508
function: _raisesoapfault
class: soap_client
type: ->
0: Parameter count must be an integer > 0, value sent: -3
1: Errno: 256 Filename: /export/asd/metallo2/metallodb/webdocs/services/soap.php Lineno: 46
2: PHP
3: SOAP-ENV:Server
args:
2:
file: /home/server/php/lib/php/SOAP/Client.php
line: 476
function: __decoderesponse
class: soap_client
type: ->
value: SOAP-ENV:Server
name: faultcode
type: QName
namespace: http://schemas.xmlsoap.org/soap/envelope/
type_namespace: http://www.w3.org/2001/XMLSchema
attributes:
arrayType:
options:
name: faultcode
ns:
namespace: http://schemas.xmlsoap.org/soap/envelope/
nqn:
name: QName
ns:
namespace: http://www.w3.org/2001/XMLSchema
tqn:
type_prefix:
0:
value: Parameter count must be an integer > 0, value sent: -3
name: faultstring
type: string
namespace: http://schemas.xmlsoap.org/soap/envelope/
type_namespace: http://www.w3.org/2001/XMLSchema
attributes:
arrayType:
options:
name: faultstring
ns:
namespace: http://schemas.xmlsoap.org/soap/envelope/
nqn:
name: string
ns:
namespace: http://www.w3.org/2001/XMLSchema
tqn:
type_prefix:
1:
value: PHP
name: faultactor
type: anyURI
namespace: http://schemas.xmlsoap.org/soap/envelope/
type_namespace: http://www.w3.org/2001/XMLSchema
attributes:
arrayType:
options:
name: faultactor
ns:
namespace: http://schemas.xmlsoap.org/soap/envelope/
nqn:
name: anyURI
ns:
namespace: http://www.w3.org/2001/XMLSchema
tqn:
type_prefix:
2:
value: Errno: 256 Filename: /export/asd/metallo2/metallodb/webdocs/services/soap.php Lineno: 46
name: detail
type: string
namespace: http://schemas.xmlsoap.org/soap/envelope/
type_namespace: http://www.w3.org/2001/XMLSchema
attributes:
arrayType:
options:
name: detail
ns:
namespace: http://schemas.xmlsoap.org/soap/envelope/
nqn:
name: string
ns:
namespace: http://www.w3.org/2001/XMLSchema
tqn:
type_prefix:
3:
value:
name: Fault
type: Struct
namespace: http://schemas.xmlsoap.org/soap/envelope/
type_namespace:
attributes:
arrayType:
options:
name: Fault
ns:
namespace: http://schemas.xmlsoap.org/soap/envelope/
nqn:
name: Struct
ns:
namespace:
tqn:
type_prefix:
0:
args:
3:
file: /home/server/php/lib/php/SOAP/Client.php
line: 245
function: __parse
class: soap_client
type: ->
0: SOAP-ENV:Server Parameter count must be an integer > 0, value sent: -3 PHP Errno: 256 Filename: /export/asd/metallo2/metallodb/webdocs/services/soap.php Lineno: 46
1: UTF-8
2:
args:
4:
file: /home/jesus/devel/php/presentations/slides/mdb/test_soap.xml
line: 45
function: call
class: soap_client
type: ->
0: metallopdb
metal: zn
mode: first
count: -3
1:
2: urn:MDB_SOAP_Server
args:
5:
backtrace:
callback:

Using the metallopdb method correctly

[metal:zn][mode: random][count: 3]
metal: zn
source_id: 1eb6
revision_date: 2001/11/23
deposition_date: 2001/07/19
expdata: x-ray diffraction
r_value: 0.10
resolution: 1.00
authors: k.e.mcauley,y.jia-xing,e.j.dodson,j.lehmbeck, p.r.ostergaard,k.s.wilson
description: Header: [hydrolase 19-jul-01 1eb6] Title: [deuterolysin from aspergillus oryzae] Compound: [mol_id: 1; molecule: neutral protease ii; synonym: npii, deuterolysin; chain: a; ec: 3.4.24.39] Source: [mol_id: 1; organism_scientific: aspergillus oryzae] Keywords: [zinc, neutral protease ii, hydrolase]
0:
metal: zn
source_id: 1qf2
revision_date: 2000/12/20
deposition_date: 1999/04/06
expdata: x-ray diffraction
r_value: 0.16
resolution: 2.06
authors: j.-f.gaucher,m.selkti,g.tiraboschi,t.prange,b.p.roques, a.tomas,m.c.fournie-zaluski
description: Header: [hydrolase 06-apr-99 1qf2] Title: [thermolysin (e.c.3.4.24.27) complexed with (2-sulphanyl-3- phenylpropanoyl)-gly-(5-phenylproline). parameters for zn- monodentation of mercaptoacyldipeptides in metalloendopeptidase] Compound: [mol_id: 1; molecule: thermolysin; chain: a; ec: 3.4.24.27] Source: [mol_id: 1; organism_scientific: bacillus thermoproteolyticus] Keywords: [zn metallopeptidase]
1:
metal: zn
source_id: 1xuf
revision_date: 1998/12/16
deposition_date: 1997/10/10
expdata: x-ray diffraction
r_value: 0.15
resolution: 2.04
authors: b.a.katz,j.m.clark,j.s.finer-moore,t.e.jenkins,c.r.johnson, m.j.rose,c.luong,w.r.moore,r.m.stroud
description: Header: [serine protease 10-oct-97 1xuf] Title: [trypsin-babim-zn+2, ph 8.2] Compound: [mol_id: 1; molecule: trypsin; chain: null; ec: 3.4.21.4; other_details: trypsin/zn+2/small molecule ligand complex] Source: [mol_id: 1; organism_scientific: bos taurus; organism_common: bovine] Keywords: [trypsin-zn+2-small molecule ligand, designed small molecule ligand with nanomolar affinity]
2:

Using the rssmetallopdb method

[metal: zn][mode: last][count: 3] 
<?xml version="1.0" encoding="iso-8859-1"?>
<rdf:RDF 
         xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
         xmlns="http://purl.org/rss/1.0/"
         xmlns:mn="http://usefulinc.com/rss/manifest/"
         xmlns:dc="http://purl.org/dc/elements/1.1/"
>

  <channel rdf:about="http://metallo.scripps.edu/services/soap.php">
    <title>MDB - The Metalloprotein Database and Browser</title>
    <link>http://metallo.scripps.edu</link>
    <description>Data retrieved using the MDB API</description>
    <items>
      <rdf:Seq>
        <rdf:li rdf:resource="http://metallo.scripps.edu/remote/remote.php3?source_id[]=9nse&amp;metal[]=zn" />
        <rdf:li rdf:resource="http://metallo.scripps.edu/remote/remote.php3?source_id[]=9icv&amp;metal[]=zn" />
        <rdf:li rdf:resource="http://metallo.scripps.edu/remote/remote.php3?source_id[]=9ici&amp;metal[]=zn" />
      </rdf:Seq>
    </items>
  </channel>

  <item rdf:about="http://metallo.scripps.edu/remote/remote.php3?source_id[]=9nse&amp;metal[]=zn">
    <link>http://metallo.scripps.edu/remote/remote.php3?source_id[]=9nse&amp;metal[]=zn</link>
    <title>(Zn) 9nse [deposited on: 1999/01/13, revised on: 2000/10/25]</title>
    <description>Header: [oxidoreductase 13-jan-99 9nse]
Title: [bovine endothelial nitric oxide synthase, ethyl- isoselenourea complex]
Compound: [mol_id: 1; molecule: nitric oxide synthase; chain: a, b; fragment: heme domain; synonym: nos, enos; ec: 1.14.13.39; engineered: yes]
Source: [mol_id: 1; organism_scientific: bos taurus; organism_common: bovine; cell: endothelial; expression_system: escherichia coli; expression_system_common: bacteria; expression_system_strain: bl21]
Keywords: [heme protein, tetrahydrobiopterin] Authors[h.li,c.s.raman,p.martasek,v.kral,b.s.s.masters,t.l.poulos] ExpData[x-ray diffraction] R-value[0.20] Resolution[2.24]</description>
  </item>

  <item rdf:about="http://metallo.scripps.edu/remote/remote.php3?source_id[]=9icv&amp;metal[]=zn">
    <link>http://metallo.scripps.edu/remote/remote.php3?source_id[]=9icv&amp;metal[]=zn</link>
    <title>(Zn) 9icv [deposited on: 1995/12/16, revised on: 1996/11/15]</title>
    <description>Header: [complex (nucleotidyltransferase/dna) 16-dec-95 9icv]
Title: [dna polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of dna; soaked in the presence of datp (0.1 millimolar) and zncl2 (0.2 millimolar)]
Compound: [mol_id: 1; molecule: dna polymerase beta; chain: a; ec: 2.7.7.7; engineered: yes; mol_id: 2; molecule: dna (5'-d(*cp*ap*tp*tp*ap*gp*a)-3') (dot) (5'-d(*tp*cp*tp*ap*ap*tp*g)-3'); chain: t, p; engineered: yes; other_details: soaked in the presence of datp (0.1 millimolar) and zncl2 (0.2 millimolar)]
Source: [mol_id: 1; organism_scientific: homo sapiens; organism_common: human; expression_system: escherichia coli; mol_id: 2; synthetic: yes]
Keywords: [dna replication, dna repair, nucleotidyltransferase, complex (nucleotidyltransferase/dna)] Authors[h.pelletier,m.r.sawaya] ExpData[x-ray diffraction] R-value[0.18] Resolution[2.70]</description>
  </item>

  <item rdf:about="http://metallo.scripps.edu/remote/remote.php3?source_id[]=9ici&amp;metal[]=zn">
    <link>http://metallo.scripps.edu/remote/remote.php3?source_id[]=9ici&amp;metal[]=zn</link>
    <title>(Zn) 9ici [deposited on: 1995/12/15, revised on: 1996/11/15]</title>
    <description>Header: [complex (nucleotidyltransferase/dna) 15-dec-95 9ici]
Title: [dna polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of dna; soaked in the presence of dttp (1 millimolar) and zncl2 (1 millimolar)]
Compound: [mol_id: 1; molecule: dna polymerase beta; chain: a; ec: 2.7.7.7; engineered: yes; mol_id: 2; molecule: dna (5'-d(*cp*ap*tp*tp*ap*gp*a)-3') (dot) (5'-d(*tp*cp*tp*ap*ap*tp*g)-3'); chain: t, p; engineered: yes; other_details: soaked in the presence of dttp (1 millimolar) and zncl2 (1 millimolar)]
Source: [mol_id: 1; organism_scientific: homo sapiens; organism_common: human; expression_system: escherichia coli; mol_id: 2; synthetic: yes]
Keywords: [dna replication, dna repair, nucleotidyltransferase, complex (nucleotidyltransferase/dna)] Authors[h.pelletier,m.r.sawaya] ExpData[x-ray diffraction] R-value[0.17] Resolution[3.10]</description>
  </item>

  <rdf:Description rdf:ID="manifest">
    <mn:channels>
      <rdf:Seq>
        <rdf:li rdf:resource="http://metallo.scripps.edu/services/soap.php" />
      </rdf:Seq>
    </mn:channels>
  </rdf:Description>

</rdf:RDF>