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Re: [Chimera-users] Analysis of the contact maps from the MARTINI MD trajectory
by James Starlight 01 Jun '16

01 Jun '16

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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)cgl.ucsf.edu >>>>>>>>> Manage subscription: >>>>>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>>>>>> >>>>>>>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >

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suggest improvements/group viz
by Dougherty, Matthew T 31 May '16

31 May '16

1) in a group viz it would be desirable to have two cursors. A regular cursor that would operate as expected under the OS, and a second cursor that would be restricted to the view window overlay. The first cursor would be controlled by the viz operator used to adjust parameters. The second cursor would be controlled by the group through a gamepad etc, that could be used as a pointer. Possibly the volume eraser might be a quick work around. 2) volume eraser when erasing sets the density to zero. Need to be able to set the value. Zero is a valid density value, usually in the middle of the density histogram, which causes problems for volume rendering. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Rotamers in Chimera
by Lew Jacobson 31 May '16

31 May '16

I am using Chmiera 1.10 build 40304 on a Mac. (I am a leftover Midas user!) So far as I can tell, this version is still using the Dunbrack 2002 rotamer library. Is any subsequent version using the improved 2011 Dunbrack library? If not, can you instruct me how to incorporate that newer library into Chimera? thanks, Lew Jacobson -- Dr. Lewis Jacobson Professor of Biological Sciences Univ. of Pittsburgh Pittsburgh PA 15260 412-624-4647 Fax 412-624-4759 LJAC(a)pitt.edu

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Can I use wait command over Rest service?
by Mungo Carstairs (Staff) 31 May '16

31 May '16

Hi, I am trying to devise a way to highlight locations on a structure in Chimera while mousing over the sequence in Jalview. My latest attempt tries to 'flash' the side-chain display at the residue position i.e. - hide then show atoms (if currently displayed e.g. display is in atom mode) - or show then hide atoms (if currently not displayed e.g. display is in ribbon mode) I'm sending a command like display #0:30.A;wait 20;~display #0:30.A to the Rest service. However while this seems to do what I want when used at the Chimera command line, via the Rest service it ignores the wait command, with the result that the action is too quick to see. Any suggestions please for how to get this to work, or a better alternative? Thanks, Mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> The University of Dundee is a registered Scottish Charity, No: SC015096

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broken lines
by shazia sabir 29 May '16

29 May '16

Hi dear All, Why chimera is showing broken lines (region encircled in red at one area). What can we predict from structure. I attached sequence of structure that shows amino acid is there(gey region in sequence). Regards, shazia.

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Modeller awareness of other proteins
by Eiros Zamora, Juan 26 May '16

26 May '16

Dear Chimera experts, I’ve got a system of three interacting proteins, and each of them is missing some linker regions in the crystal structure. I’ve succesfully used the Modeller interface in Chimera to add these regions, but the problem I’m facing now is that it adds the residues without considering that other atoms from another protein of the system are in the way. Is there a way to tell Modeller to be sensitive to other structures nearby? Thanks for any comments, [Imperial College London] <http://www.icb-cdt.co.uk/> Juan Eiros Zamora / PhD Student je714(a)ic.ac.uk<mailto:je714@ic.ac.uk> / +44 (0) 7783018326 Imperial College London Imperial College Road SW7 2AZ | UK http://www.icb-cdt.co.uk/

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Evolutional-based analysis in Chimera
by James Starlight 25 May '16

25 May '16

Dear Chimera Users! For my particular analysis I have 2 homologue membrane proteins (one is bacterial, and another one- mammalian cytocrome-C oxydase) each bound to same smaller (ligand) protein called for simplicity "the_guy". For that particular case the conservation in sequence of both protein is quite low however 1) the overall fold of both proteins especially within the membrane-embedded region as well as 2) ligand-bound (which is mostly the water exposed loops) region are quite similar. Now using some Chimera tool I need to estimate binding interfaces of two homologous proteins in terms of the conservation of the resides involved in binding of the_guy. Then I need to make more complex task- performing the same evolutional analysis but comparing 2 ensembles extracted from the MD trajectory represent simulation of binding of each of the protein with the_guy to track correlations of the statistics between the residues involved in the binding during MD as well as overall conservation for particular fold. Does the "Evolutionary tracing" might be useful here? Thanks for help! Gleb

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PDB post-processing
by James Starlight 25 May '16

25 May '16

Dear Chimera users! After some post-processing of MD simulation I have extracted from the trajectory several snapshots as individual pdbs which I need to 1- to re-assign information regarding chain letters (which was lost after some operations on pdbs) for all of those structures assuming that within each of these pdbs residues are ordered correctly e.g from (1-104 which should be chain A) than from 1-100 (it should be chain B), than 1-70 (in should be chain C) etc. 2- superimpose and combine all of the pdbs within one model in nmr-like format. Thanks for help!

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Long-ranged electrostatics analysis
by James Starlight 25 May '16

25 May '16

Dear Chimera users! I am analysing several snapshots etracted from the full atomistic md simulation of protein-protein assosiation. I wounder to ask what are the Chiemra plugins might be useful to study long-rang electrostatic effect mediated initial recognition of both proteins in this system besides APBS caclucation which is more focused on short-ranged electrostatics. Thanks for help! Gleb

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Script to open density from Coot in Chimera.
by Oliver Clarke 23 May '16

23 May '16

Hi all, Posting this in case it is useful to anyone else who uses both programs. This script will allow Coot to open the currently displayed molecules/maps in Chimera, and adjust display settings appropriately for taking a picture of electron density. Either put the appended code in your coot.py and use from the scripting interface, or place this longer script ( https://www.dropbox.com/s/0b4bebwxw0p9x0e/oli_custom.py?dl=0) in your ~/.coot-preferences directory, which will add a new "Custom" menu including this option under the "Display" submenu (as well as a bunch of other stuff, and some extra custom key bindings). The orientation of the molecules should be correct after loading in Chimera, but the zoom and clipping may require some adjustment (I am not sure exactly how to match these precisely between the two programs). The script will only load a fragment of the maps (the same region that is displayed in Coot), but this has the advantage that it takes advantage of Coot's ability to deal with crystal symmetry, so it can be used at crystal contacts with no problems. Let me know if you run into any bugs! Cheers, Oli. Code: #Open displayed models and maps in Chimera, set map levels and view def open_in_chimera(): if find_exe("chimera"): #If chimera exists do stuff, else raise an error import subprocess pwd=os.getcwd() #Dir from which coot was launched cofr=rotation_centre() #3-membered list [x,y,z] make_directory_maybe("coot-chimera") #Put coot droppings here coot_chimera_path=pwd+"/coot-chimera/" check_path=coot_chimera_path+"chimera_launcher.cmd" #Chimera run script that will be written later check_path2=coot_chimera_path+"matrix.txt" #Orientation matrix for chimera input view_number=add_view_here("tmp") # initial_zoom=zoom_factor() #Coot's zoom factor. 100 is the initial state, zooming out gets larger, in gets smaller. # reset_view() zoom=zoom_factor() # go_to_view_number(view_number,1) # scale_factor=initial_zoom/base_zoom # chimera_scale=base_zoom/initial_zoom chimera_scale=100.0/zoom #Approx - breaks down when initial views upon loading mol in Coot or Chimera are different map_radius=get_map_radius() #We'll use this to export a map_radius sized fragment if os.path.isfile(check_path): #if chimera script exists, delete it. os.remove(check_path) if os.path.isfile(check_path2): #same for matrix.txt os.remove(check_path2) map_list=map_molecule_list() mol_list=model_molecule_list() matrix_list=view_matrix() #9-membered list of rotation matrix elements. with open(check_path2,"a") as matrix_file: #Write orientation matrix (specify first pdb as model, then use matrixcopy to apply to all others). Translation vector in last column is 0,0,0 because we will take care of that separately. matrix_file.write("Model {model_id}.0\n".format(model_id=mol_list[0])) matrix_file.write("\t {a} {b} {c} 0.0\n".format(a=matrix_list[0],b=matrix_list[1],c=matrix_list[2])) matrix_file.write("\t {a} {b} {c} 0.0\n".format(a=matrix_list[3],b=matrix_list[4],c=matrix_list[5])) matrix_file.write("\t {a} {b} {c} 0.0\n".format(a=matrix_list[6],b=matrix_list[7],c=matrix_list[8])) with open(check_path,"a") as cmd_file: #Start writing stuff to chimera launch script. for mol_id in model_molecule_list(): if mol_is_displayed(mol_id): file_name=coot_chimera_path+"mol_{mol_id}.pdb".format(mol_id=mol_id) write_pdb_file(mol_id,file_name) path_to_file=file_name model_id=mol_id cmd_file.write("open #{model_id} {mol}\n".format(model_id=model_id,mol=path_to_file)) cmd_file.write("color gold #{model_id}; color byhet #{model_id}; ca_and_sidechains #{model_id}; disp ~protein\n".format(model_id=model_id)) cmd_file.write("matrixset matrix.txt\n") cmd_file.write("matrixcopy #{mol_id0} #{mol_id}\n".format(mol_id0=mol_list[0],mol_id=model_id)) map_id0=mol_id for map_id in map_molecule_list(): if map_is_displayed(map_id): map_level=get_contour_level_absolute(map_id) if map_is_difference_map(map_id): model_id=map_id0+map_id #make sure that the assigned model number of each map is unique and does not overlap with those of pdbs. if map_id==0: model_id=model_id+1 file_name=coot_chimera_path+"diff_map_{model_id}.mrc".format(model_id=model_id) path_to_file=file_name export_map_fragment(map_id,cofr[0],cofr[1],cofr[2],map_radius,file_name) cmd_file.write("open #{model_id} {diff_map} \n".format(model_id=model_id,diff_map=path_to_file)) cmd_file.write("volume #{model_id} capfaces false style mesh meshlighting false squaremesh false color \"#08882eefa222\" step 1 ; sop cap off ; set depthCue ; set dcStart 0.2 ; set dcEnd 1 ; background solid white ; set showcofr ; cofr view ; clip on; volume #{model_id} level -{map_level} color #da1200000000 level {map_level} color #0000bda00000 \n".format(model_id=model_id,map_level=map_level)) cmd_file.write("matrixset matrix.txt\n") cmd_file.write("matrixcopy #{mol_id0} #{model_id}\n".format(mol_id0=mol_list[0],model_id=model_id)) else: model_id=map_id0+map_id if map_id==0: model_id=model_id+1 file_name=coot_chimera_path+"map_{model_id}.mrc".format(model_id=model_id) export_map_fragment(map_id,cofr[0],cofr[1],cofr[2],map_radius,file_name) path_to_file=file_name cmd_file.write("open #{model_id} {map} \n".format(model_id=model_id,map=path_to_file)) cmd_file.write("volume #{model_id} capfaces false style mesh meshlighting false squaremesh false color \"#08882eefa222\" step 1 ; sop cap off ; set depthCue ; set dcStart 0.2 ; set dcEnd 1 ; background solid white ; set showcofr ; cofr view ; clip on; volume #{model_id} level {map_level} \n".format(model_id=model_id,map_level=map_level)) cmd_file.write("matrixset matrix.txt\n") cmd_file.write("matrixcopy #{mol_id0} #{model_id}\n".format(mol_id0=mol_list[0],model_id=model_id)) cmd_file.write("~sel; cofr {x},{y},{z} coordinatesystem #{mol_id0}; ac mc; center sel; cofr sel; clip hither 5 fromCenter true; clip yon -5 fromCenter true; cofr view; ~set showcofr; del sel; scale {chimera_scale}".format(x=cofr[0],y=cofr[1],z=cofr[2],mol_id0=mol_list[0],chimera_scale=chimera_scale)) chimera_exe=find_exe("chimera") info_dialog("Opening in Chimera...\nOrientation should be right but you will probably need to \nadjust the scale and clipping to get the same view as in Coot. \n If you can't see anything, try zooming out.") subprocess.Popen(["chimera",check_path]) else: info_dialog("Sorry, you need UCSF Chimera installed and accessible from the terminal for this to work!") #This works okay, though adjustment of zoom and clipping still not ideal. #would it be possible to add a subprocess.communicate() to use Coot as a controller for Chimera?

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