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

James Starlight jmsstarlight at gmail.com
Thu May 19 03:42:55 PDT 2016


Update:

Assuming that contact map based approach gave me some basic clues
regarding interaction patterns established between 2 proteins - which
are mostly based on the short-ranged forces e.g mainly vdw surface
between hydrophobic side-chains from both proteins involved in the
association. Now I'd like to focus on the long-ranged  interactions -
mainly mediated by local and global (assuming that concentrations of
ions is very high in my system) electrostatics effect. What Chimera's
tools might be useful here e.g computation of the electrostatic
surface etc?

Thanks!

Gleb

2016-05-19 11:35 GMT+02:00 James Starlight <jmsstarlight at gmail.com>:
> Thanks again Eric!
>
> Indeed Cytoscape has produced very useful picture in my case. Below
> are some of the additional questions:
> 1- I don't understand fully what value for the "Weight interactions by
> number of H-bonds/contacts formed" should be better to use- here with
> biggest value less interaction are found even if I analyze the
> trajectory within which the complex emerged just after beginning of
> the simulation and stayed stable until the end.
> 2- Also how is better to recover from Cycoscape the precise values
> which typically found in the temporary Chimera logs
> 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    0.50169
>
> 3 -is it possible on-the-fly to select all the residues from that log
> involved in binding and map in to the 3D structure which is currently
> loaded in Chimera on which the trajectory is mapped?
>
> Thanks!
>
> Gleb
>
> 2016-05-19 2:01 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:
>> Yes, as it says in red at the top of the residue-interaction dialog, you need to install Cytoscape, install the StructureViz plugin from Cytoscape’s App Store, configure that plugin to know where Chimera is, and the run the plugin that will in turn execute Chimera.  Using that Chimera, running the residue-interaction MD analysis will show the interaction network in Cytoscape.  Clicking on nodes in the Cytoscape network will highlight the corresponding structure in Chimera (and vice versa if I remember correctly).
>>
>> —Eric
>>
>>> On May 18, 2016, at 9:02 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>>>
>>> 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
>>>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
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>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>
>>



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