#126 cealign issues

v1.5.0.4
closed-accepted
5
2012-06-06
2012-06-06
No

cealign has several minor issues:

- fails to align chains of length < 2*window+1

- if chain length is a multiple of window,
only (length-window) residues get aligned

- only evaluates every 2nd path of the
best 20 (increments k twice in the loop)

- if no alignment is found, the return value
is NULL which raises a SystemError instead
of a graceful error message

- finally, it's not possible to obtain the alignment
as an object (like with align ..., object=aln)

The attached patch fixes all of those issues.

Example for improved alignment:

version 1.5.0.3:
PyMOL>fetch 1C0M 1BCO, async=0
PyMOL>cealign 1C0M and chain B, 1BCO and chain A
RMSD 5.308865 over 152 residues

with patch:
PyMOL>fetch 1C0M 1BCO, async=0
PyMOL>cealign 1C0M and chain B, 1BCO and chain A
RMSD 4.958121 over 152 residues

Discussion

  • Thomas Holder

    Thomas Holder - 2012-06-06
     
  • Jason Vertrees

    Jason Vertrees - 2012-06-06

    Changes pushed into open source branch (revision 4001).

    * Added fix for auto complete on object names, too.

     
  • Jason Vertrees

    Jason Vertrees - 2012-06-06
    • assigned_to: nobody --> inchoate
    • milestone: --> v1.5.0.4
    • labels: --> Scientific Correctness
    • status: open --> closed-accepted
     

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