ConSurf Job Status Page - FINISHED

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Job number and title:

Job number 1496496145, titled: MHC Class I Heavy Chain (2VAA:A) - Gallery

Running Parameters:

Run progress:

• Extract sequence from PDB file
• Find sequence homologs
• Align sequences
• Select best evolutionary model
• Calculate conservation scores
• Project conservation scores onto the molecule

Running Messages:

• There are 3353 HMMER hits. 2757 of them are unique, including the query.
  The calculation is performed on a sample of 150 sequences that represent the list of homologues to the query.

• Click here if you wish to view the list of sequences which produced significant alignments, but were not chosen as hits.

• The best evolutionary model was selected to be: JTT. See details here
  

ConSurf calculation is finished:

Final Results

• View ConSurf results with NGL viewer [load results using color-blind friendly scale here]
  

• View ConSurf results with FirstGlance in Jmol [load results using color-blind friendly scale here]
  Note: FirstGlance version was updated. In case you can't see the molecule and get warnings, press OK and afterwards press Ctrl+F5 keys to reload the new version. You can read more about the issue here.
  

• View ConSurf results with Chimera (Download Chimera)

• View MSA and phylogenetic tree using WASABI and run ConSurf on sub-tree

• Multiple Sequence Alignment Color-Coded by Conservation

• Amino Acid Conservation Scores, Confidence Intervals and Conservation Colors

• Download all ConSurf outputs in a click!
  

PDB Files

• PDB File with Conservation Scores in the tempFactor field

• PDB File with ConSurf Results in its Header, for FirstGlance in Jmol; [with color-blind friendly scale]
  

Create high resolution figures

• Follow the instructions to produce a Chimera figure (For users of Chimera)
  

• Follow the instructions to produce a PyMol figure (For users of PyMol)
  

• Follow the instructions to produce a RasMol figure (For users of RasMol)
  

Sequence Data

• HMMER output (HMMER hits with E-values and pairwise alignments)
  

• Sequences Used (displayed in FASTA format, linked to sequence data-base)
  

Alignment

• Multiple Sequence Alignment
  

      Alignment details
      The average number of replacements between any two sequences in the alignment;
      A distance of 0.01 means that on average, the expected replacement for every 100 positions is 1.
      Average pairwise distance : 0.991591
      Lower bound : 0.00833929
      Upper bound : 2.21913

• Residue variety per position in the MSA (The table is best viewed with an editor that respects Comma-Separated Values)
  

Phylogenetic Tree

• Phylogenetic Tree in Newick format
  

• View Phylogenetic Tree
  

Project ConSurf scores on the protein most probable assembly

• View ConSurf results projected on PISA first model with NGL viewer [load results using color-blind friendly scale here]
  

• View ConSurf results projected on PISA first model with FirstGlance in Jmol [load results using color-blind friendly scale here]
  Note: FirstGlance version was updated. In case you can't see the molecule and get warnings, press OK and afterwards press Ctrl+F5 keys to reload the new version. You can read more about the issue here.
  

• Amino Acid Conservation Scores, Confidence Intervals and Conservation Colors

RasMol Coloring Scripts

• RasMol Coloring Script Showing Insufficient Data

• RasMol Coloring Script Hiding Insufficient Data
  

PDB Files

• PDB File with Conservation Scores in the tempFactor field

• PDB File with ConSurf Results in its Header, for FirstGlance in Jmol or Protein Explorer; [with color-blind friendly scale]
  

Create a high resolution figures

• Follow the instructions to produce a Chimera figure (For users of Chimera)
  

• Follow the instructions to produce a PyMol figure (For users of PyMol)