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

Eric Pettersen pett at cgl.ucsf.edu
Mon May 16 16:32:59 PDT 2016


The clustering is based on least-squares-fit RMSDs between corresponding atoms, and therefore global translations and rotations are irrelevant.

—Eric

> On May 16, 2016, at 9:08 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> 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
>>>>>> _______________________________________________
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>>>>>> 
>>>>>> 
> 
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