#89 pdb and short peptides

v1.6.0.0
closed-works-for-me
Thomas Holder
None
5
2013-03-29
2009-07-14
cowsandmilk
No

For some reason, the pdb decided in the latest round of remediation to take a lot of short peptides and turn them into het atoms. For our example, we'll use 2tlx, where the dipeptide of Val-Lys used to be a chain B, but is now 2 het atoms.

When you open this pdb and look at these residues using the attached pml, only the peptide bond shows up. This is because the pdb decides to put in a connect record for the peptide bond to let you know it's a dipeptide, but leaves out the other connect records, figuring you know they're amino acids. It is ugly in pymol.

This may be just as much (or more) a bug in the files being created by the PDB, but I'm looking at these files in pymol and getting annoyed.

Discussion

  • cowsandmilk
    cowsandmilk
    2009-07-14

    PML for fetching and displaying

     
    Attachments
  • set connect_mode, 3

    load 1tlx.pdb

     
  • Jason Vertrees
    Jason Vertrees
    2011-06-17

    • milestone: --> 1.4.2b1
     
  • Jason Vertrees
    Jason Vertrees
    2011-06-17

    Can you please provide a screenshot of what that script shows you? Thanks.

     
  • Thomas Holder
    Thomas Holder
    2013-03-29

    • Description has changed:

    Diff:

    --- old
    +++ new
    @@ -2,4 +2,4 @@
    
     When you open this pdb and look at these residues using the attached pml, only the peptide bond shows up.  This is because the pdb decides to put in a connect record for the peptide bond to let you know it's a dipeptide, but leaves out the other connect records, figuring you know they're amino acids.  It is ugly in pymol.
    
    -This may be just as much \(or more\) a bug in the files being created by the PDB, but I'm looking at these files in pymol and getting annoyed.
    +This may be just as much (or more) a bug in the files being created by the PDB, but I'm looking at these files in pymol and getting annoyed.
    
    • status: open --> closed-works-for-me
    • assigned_to: Thomas Holder
    • milestone: 1.4.2b1 --> v1.6.0.0
     
  • Thomas Holder
    Thomas Holder
    2013-03-29

    This was fixed somewhere between 1.0r2 and 1.3r1 (just tested those two). PyMOL does distance based connectivity by default (connect_mode setting).