Changes between Initial Version and Version 1 of Ticket #1180, comment 5


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Timestamp:
Aug 6, 2018, 12:42:25 PM (7 years ago)
Author:
Greg Couch

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  • Ticket #1180, comment 5

    initial v1  
    1 {{{
    21Hello,
    32
    … …  
    87Best,
    98Lukas
    10 
    11 On 27/07/2018, 03:20, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
    12 
    13     #1180: mmCIF reader forms no chains
    14     -----------------------------------+----------------------
    15               Reporter:  lpravda@…     |      Owner:  gregc
    16                   Type:  defect        |     Status:  accepted
    17               Priority:  blocker       |  Milestone:  0.7
    18              Component:  Input/Output  |    Version:
    19             Resolution:                |   Keywords:
    20             Blocked By:                |   Blocking:
    21     Notify when closed:                |   Platform:  all
    22                Project:  ChimeraX      |
    23     -----------------------------------+----------------------
    24    
    25     Comment (by gregc):
    26    
    27      So the daily ChimeraX can't open 1tqn-assembly-1.cif because it is
    28      confused by the there not being an entity_poly_seq table when entity_poly
    29      is present.  I've fixed that.  Note that the entity_poly_seq table is
    30      needed to reliably find gaps, entity_poly is not enough.
    31    
    32      HETATM generated correctly now for all non-standard residues.  ChimeraX
    33      doesn't look at the field in input, and I would like drop it from the
    34      mmCIF output, but it seems to be liked.
    35    
    36      Still looking into maintaining label_seq_id when reasonable.  It should be
    37      possible if there isn't any major structural editing.
    38    
    39      As for pdbe_label_seq_id, that is a possibility.  I don't know the
    40      details, but I heard that the RCSB's IHM effort is coming across the same
    41      problem of uniquely identifying solvent residues, so I hope there will be
    42      one solution for everyone to use.  Right now, ChimeraX's solution is to
    43      look at the auth_seq_id.  My preference is for actually using label_seq_id
    44      :-)
    45    
    46      And a FYI, ChimeraX already has some support for PDBe's updated mmCIF
    47      files. In the open command, you can say "open 3fx2 from pdbe_updated" and
    48      it will fetch the updated file.  In particular, we use the chem_comp_bond
    49      table.  It would be better if the chem_comp_bond table actually had bonds
    50      for every atom.  The CCD files are not complete templates, and I believe
    51      they are for a neutral pH instead of a human pH.  So frequently, there are
    52      missing hydrogens -- an example would be the missing HO5' for DT in the
    53      chem_comp_bond table in 3rec.
    54    
    55     --
    56     Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1180#comment:4>
    57     ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    58     ChimeraX Issue Tracker
    59    
    60 
    61 
    62 }}}