Associating a PDB file with a sequence in the sequence features file

Jalview Discussion
1

Hi,

Is it possible to associate a PDB file with a sequence in the sequence features file?

I use the standalone (non-browser) Jalview application and many of the sequences I show in Jalview actually represent PDB chains. I create the multiple sequence alignment , features and annotation files via a script and in such a case I thought that it would be very natural to associate these sequences with a PDB file already in the features file as a non-positional sequence feature.

Thanks,

Itamar

Itamar Borukhov, Ph.D.,
Principal Scientist, Algorithmic Research
Research & Development
Compugen Ltd.,
72 Pinchas Rosen, Tel Aviv 69512, Israel

···

Email: itamarb(at)cgen.com
Web: http://www.cgen.com
Tel: +972-3-765-8523
Fax: +972-3-765-8555

This email including any attachment may contain confidential and/or privileged information intended solely for the use of the specified addressee[s]. Its contents shall not be copied, reproduced, changed or communicated to another - either in whole or in part. If you have received this email or parts thereof in error we request that you notify us at the telephone number or email address appearing above and delete this email. Thank you.

2

Hi,

Is it possible to associate a PDB file with a sequence in the sequence features file?

I use the standalone (non-browser) Jalview application and many of the sequences I show in Jalview actually represent PDB chains. I create the multiple sequence alignment , features and annotation files via a script and in such a case I thought that it would be very natural to associate these sequences with a PDB file already in the features file as a non-positional sequence feature.

3

Hi Jim,

I’ve actually been working on some extensions to the PDB association mechanism that might help you here, thoough it’s not quite fully automated as yet. Basically, if you launch the development version of Jalview, and import a sequence alignment and then drag and drop a bunch of PDB files on to it, then Jalview will try to associate structures by matching up Sequence IDs with PDB filenames. In the future, I’d like jalview to do this without user intervention, so you could simply tell it where you keep your PDB files, and it would automatically match up any that were involved in the alignment you were viewing at the time. Is that any help ?

FWIW this sounds like something that could be pretty useful for our group as well - although more for the applet version. Would it be possible to provide a template URL (with the ID in the URL being replaced by each sequence ID) so PDB data could be served over HTTP rather than relying on access to the local filesystem?

Cheers,

···

–
Ian Sillitoe
Orengo Group

University College London