- Chimera-dev - RBVI Mailing Lists

apple events
by Dougherty, Matthew T 09 Dec '13

09 Dec '13

I was nosing around the code and I noticed something about an apple events handler. Wondering if this be applied to some of my development. Could you elaborate on its current use and potential application? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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creating an extension
by Dougherty, Matthew T 09 Dec '13

09 Dec '13

Hi, I am trying to create a simple extension that has a column of buttons (qty 10-20) having a corresponding column of user defined text blocks. When I push a button, the corresponding text string will be read and processed as a command string (eg, "reset default", "rock X 3", "move Z 2000") I started with VolumePlanes and whittled it down to the nub to figure out what it was doing relative to what I want; below. I am realizing the buttons defined by this example extension uses some specific chimera GUI strategies. My going with a row of buttons would work as in this volumeplanes example, but is second preference on layout. More visually intuitive to have it side by side. Not sure this is possible with another dozen lines of code, or if I would need to go about it another route using different CGLTk api's and scrap using this volumeplane extension as a boiler plate. So I am realizing that this is putting me into the intricacies of CGLtk. An alternate would be to go with std python gui code. I also know you are reinventing chimera, one reason being the tk libraries, which opens up a third approach. So I am at a crossroad as to how to proceed. Because the code is relatively small, a rewrite for chimera2 does not seem an issue. Also there are some issues with parenting I am unfamiliar with (eg, t.withdraw(), columnconfigure). I am thinking this might be a good example of an extension for a beginner, so writing it as such might be useful for others. Particularly for new developers trying to sort out the boundaries between python, chimera, tk, and the extension linkages. Need some direction as to which way to go for the least amount of work of coding. thanks, Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine =========== # ----------------------------------------------------------------------------- import chimera from chimera.baseDialog import ModelessDialog import ButtonCommands # ----------------------------------------------------------------------------- class Button_Commands_Dialog(ModelessDialog): title = 'Button Commands' name = 'button commands' buttons = ('C1', 'C2', 'C3','Close',) # --------------------------------------------------------------------------- # --------------------------------------------------------------------------- def fillInUI(self, parent): t = parent.winfo_toplevel() self.toplevel_widget = t t.withdraw() parent.columnconfigure(2, weight = 2) from CGLtk import Hybrid ps = Hybrid.Scale(parent, 'Cmd1', 0, 10, 1, 0) ps.frame.grid(row = 2, column = 0, sticky = 'ew') ps.callback(self.change_plane_cb) ps.entry.bind('<KeyPress-Return>', self.change_plane_cb) self.plane = ps def change_plane_cb(self, full_size = False): return # --------------------------------------------------------------------------- # --------------------------------------------------------------------------- def C1(self): c_1='echo c1' chimera.runCommand(c_1) def C2(self): c_2='echo c2' chimera.runCommand(c_2) def C3(self): c_3='echo c3' chimera.runCommand(c_3) # ----------------------------------------------------------------------------- def Button_Commands_dialog(create = False): from chimera import dialogs return dialogs.find(Button_Commands_Dialog.name, create=create) # ----------------------------------------------------------------------------- def show_button_commands_dialog(): from chimera import dialogs return dialogs.display(Button_Commands_Dialog.name) # ----------------------------------------------------------------------------- from chimera import dialogs dialogs.register(Button_Commands_Dialog.name, Button_Commands_Dialog, replace = True)

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Re: [chimera-dev] Chimera/Python sparse matrices
by Greg Couch 06 Dec '13

06 Dec '13

On 8/13/2010 12:06 PM, Forbes J. Burkowski wrote: > What are the steps that need to be taken if the Python used in Chimera is > to have the ability to import functions from SciPy or PySparse? > > Thanks for any advice that you can provide. > > Cheers, > Forbes Burkowski If you want to use prebuilt SciPy binaries with chimera, you need one that is compatible with the version of chimera that chimera is using. Chimera 1.4.x uses Python 2.5, and the daily builds use Python 2.7. You would add those packages to chimera by either (1) given the '--pypath dir' command line option, (2) setting your CHIMERAPTH environment variable (instead of PYTHONPATH, PYTHONPATH is ignored so chimera won't be accidentally broken by other installed Pythons), or (3) add the installation directory to sys.path in Python. If you're not using a daily build on Linux, then you should edit CHIMERA/share/chimeraInit.py and comment out or remove the part that sets the RTLD_GLOBAL flag -- it appears to be no longer needed and its presence breaks SciPy. If you're going to compile from source, which you'll need to do if you're using a daily build, I'd recommend trying PySparse first, since it is a smaller package. Python packages that incorporate C (or C++ or Fortran) code are more difficult than prebuilt binaries because (a) you need a compiler, and (b) if the code calls the Python C API, you need a compatible compiler, ideally the same one as what the rest of Chimera was build with. PySparse needs BLAS and LAPACK libraries and optionally wants UMFPACK and/or SuperLU. On on Redhat and Fedora Linux, you can get the first three libraries by installing the blas-devel, lapack-devel, and suitesparse-devel packages. Chances are you'll be able to install PySparse into chimera's python by running "CHIMERA/bin/pythonXXX setup.py install" in the pysparse source tree (where CHIMERA is the path to where chimera was installed). On Linux, you might have to set the LD_LIBRARY_PATH environment variable to CHIMERA/lib. On Mac OS X, the path to the chimera binary is CHIMERA/Contents/Resources/bin/pythonXXX and the environment variable is DYLD_LIBRARY_PATH. Or you could install PySparse into another Python and use the --pypath/CHIMERAPATH/sys.path approach as given above. Hope this helps, Greg

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Numpy multiarray import problem
by Mateusz Dobrychłop 05 Dec '13

05 Dec '13

Dear Chimera Team, I am working on my own Chimera Extension. After succesful installation of BioPython using Chimera's Python copy, I've encountered another BioPython - related problem, that is also related to the numpy library. I'm trying to import something from the BioPython library, and BioPython is trying to import from numpy. I recieve a following error: RuntimeError: module compiled against API version 8 but this version of numpy is 7 ... File "/home/mateusz/pyry4.4/Modules/Trans/ComponentRepresentation.py", line 6, in <module> from Bio.PDB import PDBParser, PDBIO, NeighborSearch File "/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/PDB/NeighborSearch.py", line 10, in <module> from Bio.KDTree import KDTree File "/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/KDTree/__init__.py", line 10, in <module> from KDTree import KDTree File "/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/KDTree/KDTree.py", line 20, in <module> from Bio.KDTree import _CKDTree <type 'exceptions.ImportError'>: numpy.core.multiarray failed to import I tried to install numpy the same way I installed BioPython (using Chimera's Python copy), but this does not solve the problem. I also tried to import numpy.core.multiarray directly in Chimera's IDLE and it did import. I'm using Chimera 1.8.1 on Ubuntu 12.10 (64 - bit). Is there anything I can do to make it work? Best wishes, Mateusz

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Re: [chimera-dev] camera positions
by Tom Goddard 05 Dec '13

05 Dec '13

Hi Matt, Take a look at the _savePosition() routine in chimera/share/Midas/__init__.py that defines the contents of each position: return ( viewer.scaleFactor, viewer.viewSize, cam.center, cam.nearFar, cam.focal, xforms, clips, om.cofrMethod, cofr, viewer.clipping, cam.fieldOfView, ) These are the fields you see in the session file. Notice it has the camera focal plane position (cam.focal) but no eye separation parameter. Tom On Dec 5, 2013, at 5:09 AM, "Dougherty, Matthew T" wrote: > Hi Tom, > > I was looking at a typical savepos as it is saved as a session file, below > > Can you tell me how to interpret it contents? Trying to understand what parameters are kept. > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > > > > def restoreMidasBase(): > formattedPositions = {'cPos': (1.0, 5.706403395613076, (105.314, 50.822, 41.951), (43.72859999036789, 40.17340000963211), 41.951, {(0, 0): ((0.0, 0.0, 0.0), (0.0, 0.0, 1.0, 0.0))}, {(0, 0, 'Molecule'): (False, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, False, 5.0)}, 4, (105.314, 50.822, 41.951), False, 7.8352333034904085)} > import Midas > Midas.restoreMidasBase(formattedPositions) >

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adjust contour to mass
by Martin Turk 26 Nov '13

26 Nov '13

Hi, I am trying to write a simple python script that will iterate over opened volumes and adjust the contour level to a certain mass. This shouldn't be more than ~10 lines. However, I can't find chimera's python library reference to look up the class structure and operator names. Does someone know how, for example, set volume level to 0.01 would look like in python? in the command line it would be for all models: volume #0-99 level 0.01 for models I've found chimera.openModels and then you can list over them, but that's about it. Thanks, Martin Turk

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FYI: Chimera crashes X-Server (solved - Nvidia driver problem)
by Wolfgang Lugmayr 19 Nov '13

19 Nov '13

Hi, Probably you know already, but I found nothing like this in the list archive. Short version: Use Nvidia driver version 319.49 on Linux when running Chimera. Long version: I've setup a new PC with Scientific Linux 6.4 and the latest Nvidia driver v319.60. Simple configuration (no stereo). When running Chimera (official builds 1.8 and 1.8.1) the X-Server crashed and logged me out somewhere after the first pop-up window (Loading Tix ...). I recompiled the latest SVN version (1.9_b39272), but still the same effect. Running the program with --debug-opengl showed no pop-up window on my system as on other older Linux PCs. Debugging the program led to a section in Tkinter/Togl part until the server crashes and gives me the login screen. So I assumed it has more to do with Tk than with Chimera. I've made a gdb remote debug session with my X-Server (see screenshot). Based on this info I made a Internet search and more programs have a similar problem with newer versions of the Nvidia driver. All infos recommend the stable 319.49 version. After this driver installation and a reboot - everything (official and my builds) work now fine. Cheers, Wolfgang -- Besuchen Sie uns auf: www.uke.de _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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Intersurf QUESTION
by niko 05 Nov '13

05 Nov '13

Hello, I use CHIMERA since several years. Thank you very much for this excellent program MY QUESTION : Is it possible to save the ASCII file of the histogram generated by the "intersurf" calculation between two molecules ? Thank you very much Nicolas Papageorgiou.

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Interfacing with Chimera
by Bernard Lieberman 21 Oct '13

21 Oct '13

Hello, I'm presently writing an application that I'd like to interface with Chimera. Essentially my program will be capable of loading a specific python session with the appropriate model and then select, stylize, etc. specific residues. I'm able to generate the commands required but I'm wondering if it's best to find a way to hook the Chimera command line or if I should be going the route of editing my source py file? I'm essentially looking for the best method to have my VB6 application interface with Chimera and was looking for some suggestions if others have done this in the past. Any tips or suggestions are greatly appreciated. Thanks! *Bernard Lazarus Lieberman*

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declaring an integer to be used for the model and select command
by Moses Adenaike 08 Oct '13

08 Oct '13

Hello there! I am trying to write a python script for chimera to rotate one molecule then translate another molecule to the right. I can get the code to work when I say use select 0 and model 1. But I want to define functions Rotate and Translate and be able to parse an integer value for the model numbers: Example def Rotate (0) where 0 would be the value of a variable called model inetger then later the function would have the code runCommand("move x -1 model #modelinteger") but when I try to compile chimera says model integer is not defined. I define it outside the function as modelinteger=0 but still the same error message shows. Basically how do I get chimera to understand that my variable modelinteger is indeed an integer?

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UCSF Chimera Help
by Neil Bugeja 21 Aug '13

21 Aug '13

Dear Sir/Madam I am a student at the University of Malta and I am currently using your software to carry out homology modelling for my thesis. I have a slight problem figuring out how to dock a ligand into a receptor on the program...Is this possible or do I need to install another software? I tried looking through the available tutorials but cannot find any so far Thank you for your help Regards -- Neil Bugeja B.Pharm (Hons) IV Year Faculty of Medicine & Surgery University of Malta

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Re: [chimera-dev] Extension to export VTK format files
by Tom Goddard 08 Aug '13

08 Aug '13

Hi Shawn, Thanks, I've added your VTK export to the Chimera daily builds. Will be in tonight's builds. Tom On Aug 8, 2013, at 12:19 PM, Shawn Waldon wrote: > Hi Tom, > > Thanks for the code tips and locations! I changed my code so that it works with Multiscale surfaces and the MSMSModel surfaces. I also handle the case where a multiscale surface piece doesn't have atoms (because it was generated as part of the biological unit) now using some helper functions from the msc command. > > As far as exporting things twice, the code does technically process the molecule twice. Once, which the model it is processing is the molecule itself, it creates points for atoms and lines for bonds and gives it some model number. Then when it is processing the surface it exports the geometry and the data for the closest atom to each point (that is relevant to that surface piece, thanks for that tip), but assigns this a different model number. In VTK it is relatively straightforward to threshold on this model num and just get the data that is of interest. > > I've attached the new version of the code. Let me know if anything else needs fixing. > > Shawn > > > On Wed, Aug 7, 2013 at 1:46 PM, Tom Goddard <goddard(a)sonic.net> wrote: > Hi Shawn, > > The solvent excluded surfaces produced by the surface command or menu Actions / Surface / Show are instances of Python class MSMSModel defined in share/MolecularSurface/msurf.py. They are a subclass of SurfaceModel and the only type of Chimera surface which has a direct association between surface vertices and nearest atoms. That association is given by s.atomMap which maps vertex number (0 based) to Python atom object. > > The MultiScale surfaces are a plain SurfaceModel. I'd suggest adapting your current code to use > > > for piece in m.surfacePieces: > if hasattr(m, 'surfacePieceAtomsAndBonds'): > atoms, bonds = m.surfacePieceAtomsAndBonds([piece], create = False) > # Now export associated atom (closest among atoms) for each vertex. > … > # Now add triangles for surface piece even if it has no associated atoms > > > I didn't study your code closely but it seems you will handle molecules that belong to multiscale surfaces twice. Not sure if that will create duplicates in your vtk output. > > Tom > > > > -- > Shawn Waldon > Graduate Research Assistant > Department of Computer Science > University of North Carolina at Chapel Hill > > <ExportVTK.zip>

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Re: [chimera-dev] Extension to export VTK format files
by Tom Goddard 07 Aug '13

07 Aug '13

Hi Shawn, I opened PDB 1idi, used your code to export it to VTK, and opened it in Paraview 4.0.1 on a Mac. Couldn't get it to show anything. I don't know Paraview and that is probably the issue. Could you tell me something I could do with this Chimera VTK export? I'd like to have an idea of what it is good for before putting it into Chimera. Tom On Jul 26, 2013, at 11:45 AM, Shawn Waldon wrote: > Hi Tom, > > Here is the export code (and the ChimeraExtension.py file). Let me know if there is anything that needs fixing. > > Shawn > > > On Fri, Jul 26, 2013 at 1:15 PM, Tom Goddard <goddard(a)sonic.net> wrote: > Hi Shawn, > > The SketchBio project looks cool. We are trying to make it easy to build hypothetical models of hiv, muscle sarcomeres, fibronectin and all manner of large molecular machinery in Chimera. It is a difficult user interface problem. Graham Johnson, Sam Hertig and I are trying to move this project along. We are happy to help your efforts on this problem. > > Can you send us your Chimera VTK export code and I'll take a look. We don't have a list of coding conventions. I don't really care how you indent your lines, or capitalize your variable names. Mostly I want the user to know when an error occurs what the nature of the problem is (e.g. export can't handle surfaces) without having to ask us. > > Tom > > > > On Jul 25, 2013, at 1:32 PM, Shawn Waldon wrote: > >> Hi Tom, >> >> I don't know exactly how high quality it is. I haven't found any bugs in my latest version, but that doesn't mean they aren't there. I am fairly new to python, so there may be some subtleties that I missed. Also, do you have coding conventions listed somewhere? I have looked, but I haven't found an official list or anything. I am willing to fix it up a bit before submitting it if you can point me to a list of things to fix up. >> >> My use case is that I am writing a higher level modeling tool that uses VTK to do its graphics. I have been calling Chimera as a subprocess to get a surface to render (and now other data). See the project website for more details: http://www.sketchbio.org >> >> Shawn >> >> >> On Tue, Jul 16, 2013 at 10:49 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> Hi Shawn, >> >> That is interesting. We could put it in Chimera if the code is solid. The error reports will come to us so we need high quality code so we have time to do more than reply to bug reports. >> >> What use of molecules in VTK motivated you to write this export code? >> >> Tom >> >> >> On Jul 16, 2013, at 11:30 AM, Shawn Waldon wrote: >> >>> Hello all, >>> >>> As part of a project that I am working on, I recently wrote an extension for Chimera that exports the scene as a .vtk file which can be read into the Visualization Toolkit or Paraview. It exports atoms (points), bonds (lines) and surfaces along with other data associated with them such as the atom and residue names, residue number, position along its chain, b-factor, occupancy, etc. in a format that can be used in VTK-based applications with the default file readers. I think this could be a good thing to add to Chimera itself, so I was wondering if you would like to have the code for the extension to add to Chimera itself. >>> >>> I look forward to hearing from you, >>> -- >>> Shawn Waldon >>> Graduate Research Assistant >>> Department of Computer Science >>> University of North Carolina at Chapel Hill >>> swaldon(a)cs.unc.edu >>> _______________________________________________ >>> Chimera-dev mailing list >>> Chimera-dev(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >> >> >> >> -- >> Shawn Waldon >> Graduate Research Assistant >> Department of Computer Science >> University of North Carolina at Chapel Hill >> swaldon(a)cs.unc.edu > > > > > -- > Shawn Waldon > Graduate Research Assistant > Department of Computer Science > University of North Carolina at Chapel Hill > swaldon(a)cs.unc.edu > <ExportVTK.zip>

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Extension to export VTK format files
by Shawn Waldon 26 Jul '13

26 Jul '13

Hello all, As part of a project that I am working on, I recently wrote an extension for Chimera that exports the scene as a .vtk file which can be read into the Visualization Toolkit <http://www.vtk.org> or Paraview<http://www.paraview.org>. It exports atoms (points), bonds (lines) and surfaces along with other data associated with them such as the atom and residue names, residue number, position along its chain, b-factor, occupancy, etc. in a format that can be used in VTK-based applications with the default file readers. I think this could be a good thing to add to Chimera itself, so I was wondering if you would like to have the code for the extension to add to Chimera itself. I look forward to hearing from you, -- Shawn Waldon Graduate Research Assistant Department of Computer Science University of North Carolina at Chapel Hill swaldon(a)cs.unc.edu

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installing python module
by Ibai Gazpio 19 Jul '13

19 Jul '13

Hi all, I would like to install an external module for python called paramiko in order to perform a ssh connection in one of my applications. How could be possible to achieve that? How is the procedure to install this kind of packages? Thanks, Ibai

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Coordination bonds treated as covalent
by Jean Didier Pie Marechal 19 Jul '13

19 Jul '13

Hi guys, I am preparing a movie in which I want an organometallic compound linked to an organic one to rotate around the bound between both moieties. Do to so, I need the whole first coordination sphere of the metal and the metal itself to behave as a unique block. If I generate bonds with chimera (covalent) I can do that. Unfortunately, if I keep the session and open back, the bonds have been changed by pseudo bonds (which is actually A LOT BETTER!) but pseudo bonds does not allow the first coordination sphere to behave as a block. I wonder what is the best to solve this problem? Can atoms related by pseudobonds be set (even from the python shell) to be rigid? All the best, JD Dr. Jean-Didier Maréchal Associate Professor The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es

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Re: [chimera-dev] camera dialog
by Tom Goddard 11 Jul '13

11 Jul '13

Hi Matt, The ViewerDialog() call always constructs a new viewer. So if you want to use this code to position your two viewer and only create the second one on the first time instead of d2 = viewing.ViewerDialog(viewer = viewer) use code that checks if you already created the second viewer like this if hasattr(chimera, 'viewer2'): d2 = chimera.viewer2 else: d2 = viewing.ViewerDialog(viewer = viewer) chimera.viewer2 = d2 Tom On Jul 10, 2013, at 12:52 AM, "Dougherty, Matthew T" wrote: > here is what I have implemented. > > the first time it executes, everything is fine. > second time it executes D2 begins stacking up viewer dialog windows. > > > from chimera import dialogs > from chimera import viewing, viewer > > d = dialogs.find('View Editor', create = 1) > d.enter() > top = d.uiMaster().winfo_toplevel() > top.autoposition = False > s = top.wm_geometry() > top.wm_geometry('%dx%d+%d+%d' % (400,350,420,30)) > d.nb.raise_page('pCamera') > > d2 = viewing.ViewerDialog(viewer = viewer) > d2.enter() > top2 = d2.uiMaster().winfo_toplevel() > top2.autoposition = False > s2 = top2.wm_geometry() > top2.wm_geometry('%dx%d+%d+%d' % (400,350,10,30)) > d2.nb.raise_page('pSideView') > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ________________________________________ > From: Tom Goddard [goddard(a)sonic.net] > Sent: Tuesday, July 09, 2013 1:51 PM > To: Dougherty, Matthew T > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] camera dialog > > Hi Matt, > > The following Python will bring up a second viewing dialog with the camera and side view tabs. They both work in some simple tests with the current daily build. For some reason the second one does not have the Lighting tab. There may be other problems. It is unlikely the dialog positions and shown tabs would be saved in a session. > > from chimera import viewing, viewer > d = viewing.ViewerDialog(viewer = viewer) > > Tom > > > On Jul 8, 2013, at 3:29 PM, "Dougherty, Matthew T" <matthewd(a)bcm.edu> wrote: > >> using python is it possible to put up two camera dialogs? >> would like to have camera & sideview up at the same time, or lighting and camera up at the same time. >> >> >> Matthew Dougherty >> National Center for Macromolecular Imaging >> Baylor College of Medicine >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >> > >

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volume viewer features/suggestion
by Dougherty, Matthew T 09 Jul '13

09 Jul '13

I have starting using feature display as my default setting, putting in other features depending on project and available display space. when selecting a feature it can be difficult to get a handle on what is being presented; the window expands or reduces, feature blocks are being inserted/deleted throughout the dialog. would suggest a horizontal black line separating the feature blocks, to make the visual grouping easier to pick out. or a vertical line down the left using color to differentiate feature groups. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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camera dialog
by Dougherty, Matthew T 09 Jul '13

09 Jul '13

using python is it possible to put up two camera dialogs? would like to have camera & sideview up at the same time, or lighting and camera up at the same time. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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volume viewer/mouse
by Dougherty, Matthew T 08 Jul '13

08 Jul '13

I am trying to write some python scripts relating to volume viewer. two things I need to have are: 1) the ability to figure out what dataset is active on the volume viewer. I will manually pick that with the mouse, my python sw will process the active model in volume viewer. 2) on the selected dataset I need to know what the min/max values are. In a unrelated problem: lately I completely avoid changing the camera scale value, I always want it to be 1.0. The mouse scroll wheel changes the scale value, so I am having accidental changes to camera scale values. How do I halt wheel commands from changing scale? under preferences/mouse I have "use mouse scroll wheel" set to false. side note: I just bought a logitech G600 mouse which has 12 buttons on the mouse that can be programmed through mode (3) and shift(2) buttons to have 12*3*2 active buttons that I can set to accelerator commands. So one of my modes will be dedicated to volume viewer controls, another for stereo/dome/camera, the other is general chimera commands. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Trouble with Saving New Atom Attributes
by Juliette Cao 05 Jul '13

05 Jul '13

Hi All, I was successfully able to change a few atom types using the setattr command. I checked to see that the atoms I changed were correct (by selecting the atoms and then then clicking the IDATM type option.) I saved the .pdb file When I opened up the saved .pdb file and checked the atom types, they had reverted back to their original type. Is there a specific way to save files after using setattr command? Regards, Juliette Cao University of Houston

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Re: [chimera-dev] Rosetta cryoEM model refinement plug-in
by Tom Goddard 18 Jun '13

18 Jun '13

Hi David, Ok, I'll discuss details with Frank. Tom On Jun 18, 2013, at 11:02 AM, David Baker wrote: > Hi Tom, > > thanks for getting back to us so quickly! Ideally perhaps you could write it with our help. We've gotten requests from collaborators that we make our method available in this way. Frank is the expert and has a picture of how this could work – – perhaps the two of you could discuss? > > Best regards, > > David > > > On Jun 18, 2013, at 10:11 AM, Tom Goddard wrote: > >> Hi David, >> >> I develop the EM map tools in Chimera and am happy to discuss making a Rosetta refinement plugin. Could you tell me what setup steps you think would be done in Chimera? I guess the refinement will take minutes to hours. Do you want Chimera to show the progress during the refinement? Is there specific analysis of the refinement result that you want to show in Chimera, e.g. coloring bad fit areas red? Do you plan on writing this plugin with our help or do you want us to write it? And have you published articles on the methodology you want the plugin to follow? >> >> Tom Goddard >> >> >> On Jun 17, 2013, at 4:52 PM, David Baker wrote: >> >>> hello, we are interested in having a rosetta-cryoEM plugin to chimera that would allow users to refine models into maps with Rosetta through a button on chimera (or other simple interface). who would be good to discuss this with? thanks, David and Frank >>> _______________________________________________ >>> Chimera-dev mailing list >>> Chimera-dev(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >>> >> > >

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(no subject)
by David Baker 18 Jun '13

18 Jun '13

hello, we are interested in having a rosetta-cryoEM plugin to chimera that would allow users to refine models into maps with Rosetta through a button on chimera (or other simple interface). who would be good to discuss this with? thanks, David and Frank

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developing my own trajectory parser
by Dennis N Bromley 03 Jun '13

03 Jun '13

Hi, I apologize if this is a newbie question - I've searched for material but didn't seem to find any answers. I would like to write a plugin that allows chimera to parse up my own trajectory format. I would like it to be seekable rather than loading the whole shebang into memory at once. Is there an example trajectory parser out there or maybe someone could point me in the right direction? I saw charmm.py, which might be a good place to start, but I am not sure of which bits I need to replicate. Any pointers on a good place to begin looking would be very appreciated. thank you! -denny-

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Installing Biopython using Chimera's Python copy
by Mateusz Dobrychłop 29 May '13

29 May '13

Hello, In response to one of my older e-mails, I was instructed to install Biopython using the Python copy that comes with Chimera's installation, in order to be able to import Biopython libraries inside my Chimera plugin. Can you please explain briefly how to do that on Windows and on Ubuntu? Cheers, Mateusz

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