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

James Starlight jmsstarlight at gmail.com
Wed May 18 09:02:56 PDT 2016 

update :-)  :

as I understand for the visualization of the interaction networks this
software should be installed in advance
http://www.cytoscape.org/download.php  , right?


2016-05-18 12:54 GMT+02:00 James Starlight <jmsstarlight at gmail.com>:
> update:
> in the output I just recognized that chains are defined in each of the
> residue so it's clear for me now!
> the only question regarding digits after contact pairs e.g 0.39322
> does it something related to probability of the stability of the
> contact along the trajectory?
>
> also didn't find how is possible to map this data on the structure-
> each time I recover it from the text log like according to Chimera
> output
>
> Trajectory residue network info: [2, 'MD residue interactions',
> '/tmp/tmp3zlaFL_network.txt', '/tmp/tmpoMVMYh_nattr.txt',
> '/tmp/tmpiVRUd4_netviz.xml']
>
>
> Gleb
>
> 2016-05-18 12:33 GMT+02:00 James Starlight <jmsstarlight at gmail.com>:
>> Yep thanks so much Eric!
>> In my case the contacts have been started to be recognized both from
>> only after choosing the vdw cutoff > -4.0 A
>> and decreasing statistical (weight discard edge threshold) factor to 0.3
>> (here I am analyzing big trajectory consisted of 7 independent MD
>> trajectories for the same system merged together where both proteins
>> are present both in bound and unbound states during the progression of
>> simulation).
>>
>> Eventually I obtained
>>
>> LYS 25.A    vdw    SER 712.C    0.39322
>> CYS 14.A    vdw    TRP 1586.I    0.427119
>> HIS 33.A    vdw    ions    0.335593
>> HIS 33.A    vdw    LYS 1577.I    0.444068
>> LYS 27.A    vdw    TRP 1586.I    0.369492
>> GLU 838.C    vdw    PHE 46.A    0.444068
>> GLN 12.A    vdw    TRP 1586.I    0.501695
>> ASP 1580.I    vdw    LYS 7.A    0.318644
>> PHE 46.A    vdw    TRP 1586.I    0.491525
>> GLU 732.C    vdw    LYS 79.A    0.372881
>> PHE 46.A    vdw    solvent    0.501695
>> CYS 1584.I    vdw    HIS 26.A    0.616949
>> HIS 26.A    vdw    SER 712.C    0.423729
>> ASP 1580.I    vdw    LYS 8.A    0.305085
>> TYR 1542.I    vdw    VAL 11.A    0.311864
>> LYS 27.A    vdw    solvent    0.40678
>> THR 28.A    vdw    TYR 731.C    0.379661
>> PHE 46.A    vdw    TYR 1587.I    0.484746
>>
>> Also may I ask within this output the first column should correspond
>> to first selection, right? here the contacts was defined as between
>> atoms from chain A which is the smaller protein and the rest of the
>> system consisted of atoms of receptor.
>>
>> Thanks again!
>>
>> Gleb
>>
>> 2016-05-17 22:37 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:
>>> Well, if I were you I would go to a trajectory frame that I think should have contacts, and then bring up the Find Clashes/Contacts tool (in the Structure Analysis category of Tools) and play around with the criteria to see what yields contacts.  You might also change the atoms to sphere mode (Actions->Atoms/Bonds->sphere) to see if they have any VDW overlap or are close.  You might also measure some distances (control-click an atom, then control-shift-double-click a second atom and then pick “Show Distance” from the popup menu).  Without actual access to your data, I can’t offer any more specific suggestions.
>>>
>>> —Eric
>>>
>>>> On May 17, 2016, at 2:08 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>>>>
>>>> Thanks Eric!
>>>>
>>>> it quite strange that no interactions are found- because in my
>>>> trajectory the complex between both proteins are emerged very soon
>>>> after beginning of the simulation and is quite stable until ed of it.
>>>> Seems like the Chimera does not recognize martini's CG atoms properly.
>>>> Are there any suggestions to fix it e.g by the variations using any of
>>>> options - e.g vdw settings etc?
>>>>
>>>> Gleb
>>>>
>>>> 2016-05-17 1:32 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:
>>>>> 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
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>>>>>>>>>>> Manage subscription:
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>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>>
>>>>
>>>

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