[Chimera-users] Analysis of the contact maps from the MARTINI MD trajectory

James Starlight jmsstarlight at gmail.com
Mon May 16 06:20:13 PDT 2016


update :

already playing with the plugin MD movie and  "residue iteration
network within the trajectory" tool
just selecting atoms from the chain A as 1st selection
and other atoms from other chains as 2nd selection

running calculation (trying to varry cut-off corresponded to vdw overlap radii)

obtained error
AttributeError: 'ResInteractionDialog' object has no attribute 'markers'

  File "/opt/UCSF/Chimera64-1.10.2/share/Movie/ResInteraction.py",
line 535, in Apply
    markerSettings = [(m['xy'], m['rgba']) for m in self.markers]

See reply log for Python traceback.

Does it means that somethig special should be specified for the
MARTINI CG atoms?

Thanks !

Gleb

2016-05-16 12:13 GMT+02:00 James Starlight <jmsstarlight at gmail.com>:
> something relevant in my model:
>
> this is martini CG model consisted of big membrane protein and small
> water soluble protein. In my particular trajectory I have only atoms
> of both proteins recognized by chimera as individual chains (e.g small
> protein is chain A and the biggest is consisted of chains B-N).
>
> Gleb
>
> 2016-05-16 11:58 GMT+02:00 James Starlight <jmsstarlight at gmail.com>:
>> update:
>>
>> with the up-to-date chimera Trajectory is loaded fine
>> now the question is related to the analysis of the binding interface.
>> is it possible to make contact maps plots based on the 2 selections
>> from the input trajectory assuming that I am using martini CG model?
>>
>> Gleb
>>
>> 2016-05-16 10:39 GMT+02:00 James Starlight <jmsstarlight at gmail.com>:
>>> OK will try to update Chimera today !
>>>
>>> What chimera's tools could be useful for the contact map based
>>> analysis of md trajectories related to my case ? E.g to determine
>>> binding interface between 2 proteins from long md simulation.
>>>
>>> Gleb
>>>
>>> 2016-05-13 19:52 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:
>>>> Hi Gleb,
>>>> If you are using Gromacs 5 trajectories, you have to be using at least
>>>> version 1.10.2 of Chimera.  If you are using that version (or later), please
>>>> use “Report a Bug” in Chimera’s Help menu to file a bug report and attach
>>>> your topology file to the bug report.  Thanks!
>>>>
>>>> —Eric
>>>>
>>>> Eric Pettersen
>>>> UCSF Computer Graphics Lab
>>>>
>>>>
>>>> On May 13, 2016, at 1:46 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>>>>
>>>> Dear Chimera users!
>>>>
>>>>
>>>> I am in charge with the analysis of protein-protein association during
>>>> long molecular dynamic simulation where my system was parametrized
>>>> using MARTINI CG force field. In particularly I am interesting to
>>>> find residues on one of the protein which are crustal for the binding
>>>> interface established during this MD.
>>>> For that purpose I am trying to use Chimera to load trajectory and
>>>> corresponded tpr file using MD movie plugin and than to
>>>> map contact maps produced by Gromacs onto the 3D structure using Chimera.
>>>> The problem that Chimera does not recognize properly the trajectory
>>>> and topology. Briefly I have removed all solvent from both files
>>>> before loading them to the Chimera using editconf and gmx convert-tpr
>>>> obtaining eventually trajectory and topology with the same number of
>>>> atoms.
>>>>
>>>>
>>>> Than when I load it to Chimera that is the error which MD movie sent me:
>>>>
>>>> VERSION 5.0.2
>>>> using floats
>>>> version 100, generation 26
>>>> 8 atoms
>>>> Traceback (most recent call last):
>>>>  File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
>>>> line 1747, in __call__
>>>>  File "CHIMERA/share/chimera/baseDialog.py", line 328, in command
>>>>  File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK
>>>>  File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply
>>>>  File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line
>>>> 56, in loadEnsemble
>>>>  File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line
>>>> 67, in loadEnsemble
>>>>  File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 25,
>>>> in __init__
>>>>  File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 86,
>>>> in __init__
>>>>  File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line
>>>> 345, in _readTopology
>>>>  File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line
>>>> 338, in _readString
>>>>  File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring
>>>>    raise EOFError
>>>> EOFError
>>>> EOFError
>>>>
>>>>  File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring
>>>>    raise EOFError
>>>>
>>>> See reply log for Python traceback.
>>>>
>>>> Will be thankful for any suggestions!
>>>>
>>>> Gleb
>>>> _______________________________________________
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>>>>



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