From: Ujjwal D. <uj...@eb...> - 2004-10-01 09:05:47
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We do show SCOP domains on PDB chain/chains. Please have a look at http://www.ebi.ac.uk/interpro/ISpy?ac=P02699&mode=single We have a set of pre-calculated attribute files for Astex viewer to highlight the domain. Astex viewer considers each observed residue as an object. So we have to pre-calculate the beg-end residue of the SCOP domains on the PDB chain(s) using the residue by residue mapping provided by MSD/PDB group at the EBI. If you have any questions please do not hesitate to contact us. cheers ujjwal On Fri, 1 Oct 2004, Jaime Prilusky wrote: > According to Miguel: > > If the data is not in the input file then Jmol probably cannot do > > anything. (Unless the algorithms are published and the techniques are > > generally agreed-upon) > > As I understand, the SCOP classification is been constructed manually, > so no automatic procedure is available. > > > > But has anybody already experiences with integrating SCOP into PDB and > > > the Jmol visualisation or any other kind of useful information about it? > > OCA integrates PDB and SCOP information. Take a look at > > http://bip.weizmann.ac.il/oca-bin/rasgen?pd=1brs&pr=A&jmol=1&id=d1brsa_ > > OCA is generating on the fly a 'rasmol' script from PDB abd SCOP > information that is then given to Jmol for display. > > The script source is also available on each OCA Atlas page, under > the section 'Structure-derived information' > > Jaim > > -- > Dr Jaime Prilusky | Jai...@we... > R&D Bioinformatics and Data Management | > Weizmann Institute of Science | fax: 972-8-9344113 > 76100 Rehovot - Israel | tel: 972-8-9344959 > > info URL http://bip.weizmann.ac.il/staff/jaime_prilusky.html > OCA is at http://bip.weizmann.ac.il/oca/ > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: IT Product Guide on ITManagersJournal > Use IT products in your business? Tell us what you think of them. Give us > Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more > http://productguide.itmanagersjournal.com/guidepromo.tmpl > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > Ujjwal K Das, PhD EMBL Outstation - The EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Phone: +44 1223 494 428 Fax: +44 1223 494 468 |