we use Jalview in an exercise for students to demonstrate sequence alignments. We compare the PDB structures 1V4S and 1V4T of the same protein, the latter having some missing amino acids between residues 156 and 180. The PDB file contains residues 16 to 461 (including the gap mentioned before). However, when loaded into Jalview (Version: 2.9.0b2) only residues 180 to 461 are displayed, ignoring the first domain with res. 16 to 156.
How can I display the whole sequence that is given in the PDB?
In the meantime are you able to use alternative examples that don’t have a gap in the PDB residue numbering sequence?
The good news is that there is development ongoing right now which should see SIFTS mappings used in future where available, giving the most reliable sequence to structure mapping as well as enriched annotation of sequences with known structure.
Best regards,
Mungo
The University of Dundee is a registered Scottish Charity, No: SC015096
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Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK. www.jalview.org www.compbio.dundee.ac.uk
we use Jalview in an exercise for students to demonstrate sequence alignments. We compare the PDB structures 1V4S and 1V4T of the same protein, the latter having some missing amino acids between residues 156 and 180. The PDB file contains residues 16 to 461 (including the gap mentioned before). However, when loaded into Jalview (Version: 2.9.0b2) only residues 180 to 461 are displayed, ignoring the first domain with res. 16 to 156.
How can I display the whole sequence that is given in the PDB?
Adding to Mungo’s reply, unobserved residues are currently stripped off from sequences retrieved from PDB.
If you are interested in viewing the whole sequence (observed + unobserved residues) then you may have to retrieve the original sequences via UniProt.
The UniProt ID for both 1V4T and 1V4S it is P35557. I hope this helps.
Regards,
Charles
Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu www.jalview.org www.compbio.dundee.ac.uk
we use Jalview in an exercise for students to demonstrate sequence alignments. We compare the PDB structures 1V4S and 1V4T of the same protein, the latter having some missing amino acids between residues 156 and 180. The PDB file contains residues 16 to 461 (including the gap mentioned before). However, when loaded into Jalview (Version: 2.9.0b2) only residues 180 to 461 are displayed, ignoring the first domain with res. 16 to 156.
How can I display the whole sequence that is given in the PDB?
thank you for your answers. Now I know that it is not me doing something wrong. I also remember that in earlier versions of Jalview I did not had the problem.
Thank you, Charles, for your suggestion with the Uniprot ID. We already take P35557 to show the whole sequence to the students, and compare it to 1V4T in order to explain to them why we need protein modeling to get the missing residues.
Thanks again.
Regards,
Eileen
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Dear Eileen,
Adding to Mungo’s reply, unobserved residues are currently stripped off from sequences retrieved from PDB.
If you are interested in viewing the whole sequence (observed + unobserved residues) then you may have to retrieve the original sequences via UniProt.
The UniProt ID for both 1V4T and 1V4S it is P35557. I hope this helps.
Regards,
Charles
Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu www.jalview.org
we use Jalview in an exercise for students to demonstrate sequence alignments. We compare the PDB structures 1V4S and 1V4T of the same protein, the latter having some missing amino acids between residues 156 and 180. The PDB file contains residues 16 to 461 (including the gap mentioned before). However, when loaded into Jalview (Version: 2.9.0b2) only residues 180 to 461 are displayed, ignoring the first domain with res. 16 to 156.
How can I display the whole sequence that is given in the PDB?