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@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@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@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@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@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@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@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hi Gleb, That error is fixed in the daily build and in the 1.11 release candidate, so you might want to upgrade to the latter. Anyway, it happens when no interactions are found. You could ignore the error and just be aware that the settings just used produced no interactions. —Eric

On May 16, 2016, at 6:20 AM, James Starlight <jmsstarlight@gmail.com> wrote:

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@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@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@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@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@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@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users