problem with minimization movie

Asked by Francisco García on 2013-10-27


I am using the procedure to visualize all conformations taken by the ligand during minimizations.

I generate docking.clust file where I can see translations and rotations, is the follow:

      Trans Rot Ener RmsdCA_ref Rank Weight
== 1 1 -57.4844249 0.937420362399 1 1

I use to generate the file, 1 1

But I get the following error when executing the previous script:

fran@fran:~/soft/ptools-develop/PyAttract$ 1 1
Translation file: translation.dat
Rotation file: rotation.dat
Target translation number: 1
Target rotation number: 1
Traceback (most recent call last):
  File "/home/fran/soft/ptools-develop/PyAttract/", line 103, in <module>
AttributeError: '_ptools.Rigidbody' object has no attribute 'GetCoords'


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Hi Francisco,

Thank you for the report.

This was a bug. I fixed the "" script (and also I think you should now be able to generate a pdb containing a trajectory.

Best regards,

Hi Adrien,

Thanks for the fix.

I found another bug when running the script, is the follow:

Traceback (most recent call last):
  File "/home/fran/soft/ptools-develop/PyAttract/", line 94, in <module>
  File "/home/fran/soft/ptools-develop/PyAttract/", line 90, in main
  File "/home/fran/soft/ptools-develop/PyAttract/", line 39, in irmsd
    pairlist = AttractPairList(receptor, ligref, cutoff) #pairlist created on protein backbone + side-chains
  File "pairlist.pyx", line 76, in _ptools.AttractPairList.__cinit__ (_ptools.cpp:9527)
    raise TypeError("arguments error in AttractPairList.__cinit__()")
TypeError: arguments error in AttractPairList.__cinit__()


Launchpad Janitor (janitor) said : #3

This question was expired because it remained in the 'Open' state without activity for the last 15 days.

I fixed the script in the github repository.


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