Home	Query Domains & Motifs	Browse	Query interactions	PDB & GO terms	InterPreTS
3DID: Technical Information Jmol 3did uses Jmol for the visualization of 3D structures. You need to install and enable Java as well as JavaScript for your browser in order to see the structures. Some helpful links and information: Java Downloads for All Operating Systems Enabling the Java plugin with Firefox Enabling JavaScript in Firefox How to activate JavaScript in your browser (IE, Firefox, Safari, Opera) In order to translate the molecule in space, you need to hold the Shift key pressed and double-click, then drag the cursor while holding the mouse button pressed down. Neato Neato (from the Graphviz package) is used to create the networks of interaction. Clicking on a domain in the network leads you to this domain's or motif's page. Networks can be large, you may want to disable this feature if you have a slow connection. They are disabled by default for the alphabetic lists of domains. Linking to 3DID by domain name: http://3did.irbbarcelona.org/cgi-bin/query_domain_cgi.pl?draw=graph&domain=domName by Pfam access code: http://3did.irbbarcelona.org/cgi-bin/query_pfamID_cgi.pl?draw=graph&id=accNum by motif name: http://3did.irbbarcelona.org/cgi-bin/query_peptide_cgi.pl?draw=graph&peptide=motifName Note that this will work for the motifs identified in our recent publication (Stein & Aloy, PLoS Comput Biol 2010) as well as for a subset of the motifs in ELM, namely, those for which we identified 3D structures (Stein & Aloy, 2008), but not for hand-curated instances. Leave out draw=graph if you want to link to the page without the interaction graph.

3DID: Technical Information

Jmol

3did uses Jmol for the visualization of 3D structures. You need to install and enable Java as well as JavaScript for your browser in order to see the structures. Some helpful links and information:

Java Downloads for All Operating Systems
Enabling the Java plugin with Firefox
Enabling JavaScript in Firefox
How to activate JavaScript in your browser (IE, Firefox, Safari, Opera)
In order to translate the molecule in space, you need to hold the Shift key pressed and double-click, then drag the cursor while holding the mouse button pressed down.

Neato

Neato (from the Graphviz package) is used to create the networks of interaction. Clicking on a domain in the network leads you to this domain's or motif's page. Networks can be large, you may want to disable this feature if you have a slow connection. They are disabled by default for the alphabetic lists of domains.

Linking to 3DID

by domain name: http://3did.irbbarcelona.org/cgi-bin/query_domain_cgi.pl?draw=graph&domain=domName
by Pfam access code: http://3did.irbbarcelona.org/cgi-bin/query_pfamID_cgi.pl?draw=graph&id=accNum
by motif name: http://3did.irbbarcelona.org/cgi-bin/query_peptide_cgi.pl?draw=graph&peptide=motifName
Note that this will work for the motifs identified in our recent publication (Stein & Aloy, PLoS Comput Biol 2010) as well as for a subset of the motifs in ELM, namely, those for which we identified 3D structures (Stein & Aloy, 2008), but not for hand-curated instances.

Leave out draw=graph if you want to link to the page without the interaction graph.