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

James Starlight jmsstarlight at gmail.com
Mon May 16 09:08:47 PDT 2016


update :-)

in addition to the previous question which is still actual I am
interesting in the clusterization of binding interfaces established
during MD e.g based on the position of one protein regarding another.

 For my case I have performed such clusterization from MD movie plugin
(which was based on current selection which was the atoms of smaller
protein) obtaining alot of overlapped clusters in case of smallest
step size and afew clusters increasing step size twisly. Is it
possible here to increase accuracy of the clusterization and to remove
some degrees of freedom which are not important for my case ? E.g to
pre-process trajectory using PCA before clusterization to discard
rotation translation of the system will be good option?



James

2016-05-16 15:20 GMT+02:00 James Starlight <jmsstarlight at gmail.com>:
> 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
>>>>> _______________________________________________
>>>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>>>>> Manage subscription:
>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>>>
>>>>>



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