Re: [Chimera-users] Analysis of the contact maps from the MARTINI MD trajectory
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@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@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@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@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@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 >>> >>>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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@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@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@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@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 >>>> >>>>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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@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@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@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@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@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 >>>>> >>>>>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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@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@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@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@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@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@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 >>>>>> >>>>>> > > _______________________________________________ > Chimera-users mailing list: Chimera-users@cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >
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@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@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@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@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@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@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@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@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@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 >>>>>>> >>>>>>> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users@cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >
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@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@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@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@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@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@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@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@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@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@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 >>>>>>>> >>>>>>>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users@cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> >
Hi Gleb, While not specifically for trajectories (i.e. you would have to choose an individual frame, probably wouldn’t want to try to do it on all frames), see Coulombic Structure Coloring - and/or - PDB2PQR APBS Electrostatic Surface Coloring Those are the names of the graphical-interface tools but they all also have commands, see the manual pages and links therein: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html> They are also all covered in the “Surface Properties” image tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2016, at 3:42 AM, James Starlight <jmsstarlight@gmail.com> wrote:
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
Since coloring surfaces by electrostatics depends upon assigning partial charges to individual atoms, I believe none of these tools will actually work for you since you have a Martini CG trajectory where each of the “atoms” actually represent several individual atoms. I have no idea how you would attempt to color a CG-trajectory surface by electrostatics. —Eric
On May 19, 2016, at 2:15 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Gleb, While not specifically for trajectories (i.e. you would have to choose an individual frame, probably wouldn’t want to try to do it on all frames), see
Coulombic Structure Coloring - and/or - PDB2PQR APBS Electrostatic Surface Coloring
Those are the names of the graphical-interface tools but they all also have commands, see the manual pages and links therein:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
They are also all covered in the “Surface Properties” image tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2016, at 3:42 AM, James Starlight <jmsstarlight@gmail.com> wrote:
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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Elaine, Dear Eric, thank you so much for the explanation! Indeed I suppose I should to convert my trajectory from CG to FG model firstly using back-mapping approach to proceed it to the APBS analysis. With Best Regards, Gleb 2016-05-19 23:22 GMT+02:00 Eric Pettersen <pett@cgl.ucsf.edu>:
Since coloring surfaces by electrostatics depends upon assigning partial charges to individual atoms, I believe none of these tools will actually work for you since you have a Martini CG trajectory where each of the “atoms” actually represent several individual atoms. I have no idea how you would attempt to color a CG-trajectory surface by electrostatics.
—Eric
On May 19, 2016, at 2:15 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Gleb, While not specifically for trajectories (i.e. you would have to choose an individual frame, probably wouldn’t want to try to do it on all frames), see
Coulombic Structure Coloring - and/or - PDB2PQR APBS Electrostatic Surface Coloring
Those are the names of the graphical-interface tools but they all also have commands, see the manual pages and links therein:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
They are also all covered in the “Surface Properties” image tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2016, at 3:42 AM, James Starlight <jmsstarlight@gmail.com> wrote:
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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Chimera Users! Also what I am interesting to ask regarding Network view of contact maps done via Cytoscape + Chimera: In principal I have no problems with such analysis of the MD trajectory however having some unsertainly in the statistical theresholds which should be set by user in the histogram upon the analysis of the contact maps. 2) Now I would like to do the same but now for trajectories but for the selected snapshots from the trajectory and compare them vizually. In chimera it is possible just to calculate contact for the pairs of residues defined in the selection (find clashes/contacts) for each of the pdb. Is it possible to do the same including Cytoscape to obtain networks for each of the pdb under analysis? Thanks! Gleb 2016-05-19 12:42 GMT+02:00 James Starlight <jmsstarlight@gmail.com>:
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@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@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@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@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@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@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@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@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@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@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 >>>>>>>>> >>>>>>>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list: Chimera-users@cgl.ucsf.edu >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >
Hi Gleb, If you are using the approach where you first start Cytoscape, use it to start Chimera, and then use the MD Movie tool to show the network, the residue interaction network (RIN) contacts-parameters dialog has options to limit the calculation to the selection. Even though you would still be using MD Movie with the trajectory, in the first RIN dialog you could specify only using a single specific frame (snapshot). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#rins> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#rin-contacts> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 24, 2016, at 9:51 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera Users!
Also what I am interesting to ask regarding Network view of contact maps done via Cytoscape + Chimera:
In principal I have no problems with such analysis of the MD trajectory however having some unsertainly in the statistical theresholds which should be set by user in the histogram upon the analysis of the contact maps.
2) Now I would like to do the same but now for trajectories but for the selected snapshots from the trajectory and compare them vizually.
In chimera it is possible just to calculate contact for the pairs of residues defined in the selection (find clashes/contacts) for each of the pdb. Is it possible to do the same including Cytoscape to obtain networks for each of the pdb under analysis?
Thanks!
Gleb
Thank you for the information, Elaine! As I found it's possbile to narrow frame range to 2 frames, defining first and last frames for calculations of the contacts from the MD movie plugin. Does it meas that it will compare contacts from those 2 given snapshots and not for only 1 selected snapshot? Also how is better operate with the selection of the statistical thresholds on the stage of the visualization of the contact calculations via cytoscape networks? Thanks! Gleb 2016-05-25 20:29 GMT+02:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi Gleb, If you are using the approach where you first start Cytoscape, use it to start Chimera, and then use the MD Movie tool to show the network, the residue interaction network (RIN) contacts-parameters dialog has options to limit the calculation to the selection. Even though you would still be using MD Movie with the trajectory, in the first RIN dialog you could specify only using a single specific frame (snapshot).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#rins> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#rin-contacts>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 24, 2016, at 9:51 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera Users!
Also what I am interesting to ask regarding Network view of contact maps done via Cytoscape + Chimera:
In principal I have no problems with such analysis of the MD trajectory however having some unsertainly in the statistical theresholds which should be set by user in the histogram upon the analysis of the contact maps.
2) Now I would like to do the same but now for trajectories but for the selected snapshots from the trajectory and compare them vizually.
In chimera it is possible just to calculate contact for the pairs of residues defined in the selection (find clashes/contacts) for each of the pdb. Is it possible to do the same including Cytoscape to obtain networks for each of the pdb under analysis?
Thanks!
Gleb
On May 30, 2016, at 8:54 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Thank you for the information, Elaine!
As I found it's possbile to narrow frame range to 2 frames, defining first and last frames for calculations of the contacts from the MD movie plugin. Does it meas that it will compare contacts from those 2 given snapshots and not for only 1 selected snapshot?
Yes, in that case it will use both snapshots. However, what you can do is put in a “stride” value large enough that the start value plus the stride is immediately larger than the last frame. In that case, only the starting frame will be used.
Also how is better operate with the selection of the statistical thresholds on the stage of the visualization of the contact calculations via cytoscape networks?
I’m not sure what you’re asking here. Maybe you could rephrase the question? —Eric Eric Pettersen UCSF Computer Graphics Lab
Thanks!
Gleb
2016-05-25 20:29 GMT+02:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi Gleb, If you are using the approach where you first start Cytoscape, use it to start Chimera, and then use the MD Movie tool to show the network, the residue interaction network (RIN) contacts-parameters dialog has options to limit the calculation to the selection. Even though you would still be using MD Movie with the trajectory, in the first RIN dialog you could specify only using a single specific frame (snapshot).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#rins> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#rin-contacts>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 24, 2016, at 9:51 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera Users!
Also what I am interesting to ask regarding Network view of contact maps done via Cytoscape + Chimera:
In principal I have no problems with such analysis of the MD trajectory however having some unsertainly in the statistical theresholds which should be set by user in the histogram upon the analysis of the contact maps.
2) Now I would like to do the same but now for trajectories but for the selected snapshots from the trajectory and compare them vizually.
In chimera it is possible just to calculate contact for the pairs of residues defined in the selection (find clashes/contacts) for each of the pdb. Is it possible to do the same including Cytoscape to obtain networks for each of the pdb under analysis?
Thanks!
Gleb
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On May 31, 2016, at 4:44 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
On May 30, 2016, at 8:54 AM, James Starlight <jmsstarlight@gmail.com> wrote:
As I found it's possbile to narrow frame range to 2 frames, defining first and last frames for calculations of the contacts from the MD movie plugin. Does it meas that it will compare contacts from those 2 given snapshots and not for only 1 selected snapshot?
Yes, in that case it will use both snapshots. However, what you can do is put in a “stride” value large enough that the start value plus the stride is immediately larger than the last frame. In that case, only the starting frame will be used.
Just to clarify, stride = step size Elaine
The last-column number is, by default, the percentage of frames that the residue pair met the interaction criteria. If you had changed “Weight interactions by number of H-bonds/contacts formed” to true, then that number would be multiplied by the number of H-bonds/contacts per frame (for frames that had any). —Eric
On May 18, 2016, at 3:54 AM, James Starlight <jmsstarlight@gmail.com> wrote:
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@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@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@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@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@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@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 >>>>> >>>>>
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participants (3)
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Elaine Meng -
Eric Pettersen -
James Starlight