March 2014 - Chimera-dev - RBVI Mailing Lists

tangent wave
by Dougherty, Matthew T 27 Mar '14

27 Mar '14

Hi, I just purchased a Tangent Wave that I plan to interface into chimera. The best design is to use sockets. Is there any precedence for using sockets in chimera? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Re: [chimera-dev] S3D extension
by Tom Goddard 20 Mar '14

20 Mar '14

Hi Matt, Yes, unfortunately Chimera dialogs often do not track changes to the underlying parameters they are displaying. So if you want to directly control the Camera dialog settings for screen width, here is the Python code to get the ViewerDialog (which holds the Camera pane, Effects pane, Side View pane, …). >>> from chimera import dialogs >>> from chimera.viewing import ViewerDialog >>> d = dialogs.find(ViewerDialog.name) <chimera.viewing.ViewerDialog object at 0x10d6ebfd0> >>> d.screenWidth.get() 35.55118110236221 >>> d.screenWidth.set(45) The Tangent Wave looks fun. In getting work done with Chimera we don't venture beyond keyboard, mouse/trackpad input controls. But I can see how a specialized task like making videos can benefit from the extra dedicated knobs, trackballs and buttons. Unfortunately since any input device beyond keyboard, mouse, trackpad is rare, the more exotic devices don't get much support from software developers like us. That leaves you with the tricky task of trying to hook it up to work with our software. Sorry about that. Tom On Mar 20, 2014, at 4:15 PM, "Dougherty, Matthew T" wrote: > Hi Tom, > > I tried ScreenMMWidth last night but it produces anomalous results. > When I get the value using ScreenMMWidth it matches the gui screen size value. > > When I set the value using getScreenMMWidth, the gui value does not change, but distance to screen gui value changes. > Afterwards I get the value for screen width, which matches what I set, but does not match the gui value. > > using the hack similar to what you mentioned, I can set the value in the gui correctly. > But I could not figure out how to get the viewer1 dialog handle. > That is, I can create a second viewer and do the hack. > > Being able to modify gui values directly as though I used a mouse or keyboard, as a developer outside the chimera tent, this would be preferred. Conceptually this is easier than learning/fishing for the intricacies of gui callbacks and related functions. There is going to be latency, but frequently this is not a problem. > > ===== > On a related note, I bought one of these for evaluation: > http://www.tangentwave.co.uk/products_wave.asp > > I think this maybe the one-stop HID I have been looking for to handle coordinate xforms, volume rendering, S3D, and misc project management issues. <$1500. > it can also double duty on a variety of other apps, particularly color and video editing for linux, mac, windows. > > Besides the method of keyboard accelerators (which I may not need), I will be able to directly interact with it through sockets, so I will need some help devising a strategy to manage these realtime events within chimera, registering callbacks for socket events. With this device I will have three trackballs so using the hack you mention would not be good because of latency. I should get it next week. If it looks promising and could be fielded in the lab, I could get another one and send it to CGL for evaluation. > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ________________________________________ > From: Tom Goddard [goddard(a)sonic.net] > Sent: Thursday, March 20, 2014 5:42 PM > To: Dougherty, Matthew T > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] S3D extension > > Hi Matt, > > from chimera import tkgui > tkgui.setScreenMMWidth(w) > w = tkgui.getScreenMMWidth() > > Here MM stands for millimeters. > > In general you don't want your Python code to find graphical user interface controls (entry fields, sliders, …) and modify their values. Instead you modify the parameter values and the graphical user interface should detect the change and update themselves. The case of the Icosahedron tool is just a hack where only the graphical user has access to the radius parameter. > > Tom > > > On Mar 19, 2014, at 11:13 PM, "Dougherty, Matthew T" wrote: > >> Now that I am working on a similar problem it may have a similar solution to the previous email. >> >> Specifically I am trying to add an extension to control eye seperation in animations. >> >> using the icosahedron extension as a reference, I figure I need to make a similar gui call in def set_s3d(es), and change the gui to the camera tab. >> >> # ----------------------------------------------------------------------------- >> # >> def change_s3d(start, last, step): >> range = (start, last, step) >> import Transition >> Transition.show_transition(set_s3d, range) >> >> # ----------------------------------------------------------------------------- >> # >> def set_s3d(es): >> import Transition >> Transition.show_label('eye separation', 'r = %.0f' % es) >> import Icosahedron.gui >> d = Icosahedron.gui.icosahedron_dialog() >> if d: >> d.radius.set_value(es) >> >> # ----------------------------------------------------------------------------- >> # >> import Transition >> arg_specs = (('es1', float), >> ('es2', float), >> ('frames', int)) >> >> add_transition_command('s3d', >> change_s3d, >> arg_specs, >> None, None) >> >> # ----------------------------------------------------------------------------- >> # ----------------------------------------------------------------------------- >> >> >> >> >> >> >> Matthew Dougherty >> National Center for Macromolecular Imaging >> Baylor College of Medicine >> ________________________________________ >> From: Dougherty, Matthew T >> Sent: Thursday, March 20, 2014 12:20 AM >> To: chimera-dev(a)cgl.ucsf.edu >> Subject: screen width >> >> I would like to set and get the parameter screen width. can you advise on the proper way? >> >> thx >> >> >> 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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screen width
by Dougherty, Matthew T 20 Mar '14

20 Mar '14

I would like to set and get the parameter screen width. can you advise on the proper way? thx Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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changing the radius value on volumeEraser
by Dougherty, Matthew T 10 Mar '14

10 Mar '14

Using python I would like to determine the eraser radius, calculate a new radius and update the widget. I can modify the radius value, but unable to update the parameter on the widget. Using this from VolumeEraser.gui import Volume_Eraser_Dialog v=Volume_Eraser_Dialog() r=v.sphere_radius_scale.value() print r r=r*0.5 v.sphere_radius_scale.set_value(r) If I have a widget radius of 8000,it accesses a default value of 2 rather than the value in the dialog box, and changes the sphere radius to 1. printing v I get the impression that I am access a different widget/gui. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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volume eraser
by Dougherty, Matthew T 07 Mar '14

07 Mar '14

Hi, I need some help as to how to call Erase() from VolumeEraser I am thinking it is something like this, but I am unable to determine what xxxxx value should be. from VolumeEraser.gui import Volume_Eraser_Dialog Volume_Eraser_Dialog.Erase(xxxxx) Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Re: [chimera-dev] how can i delete solovent and ligand from pdb file?
by Eric Pettersen 03 Mar '14

03 Mar '14

Hi, The issue is that a bunch of the relevant code isn't in Python -- it's in C++. It might simply be easier to use the criteria outlined in the "Automatic Categories" table in the surface command help page (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html) to implement the ligand/solvent identification yourself. Nonetheless, the Python part of the code that identifies ligands and solvent is in the 'categorize' method found in <your Chimera installation>/share/Categorizer/__init__.py. There are various calls into C++ but most of them are trivial and are obvious as to what they do and are only there to make the routine faster (since it is called for every model that is opened). The one that is not so obvious is "roots = model.roots(1)" which calculates the "roots" of each graph component of the molecule (i.e. each molecular fragment that is not connected by covalent bonds to any other fragment). The source code for computing roots is in Molecule::mg_traversalOrganize() in libs/_molecule/Molecule.cpp of the C++ source code. You can fetch the source code via git. Details about that are here: Source Code for UCSF Chimera --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Mar 2, 2014, at 5:24 PM, unwicky wrote: > Thank for your attention!I have found the two commands,and I did so,but to do this,I must load all of chimera,that's too heavy,I hope I can get the pure code,thank you again! > > > > > At 2014-02-27 05:37:25,"Eric Pettersen" <pett(a)cgl.ucsf.edu> wrote: > On Feb 24, 2014, at 6:44 AM, unwicky <unwicky(a)126.com> wrote: > >> hello,i want to delete solvent and ligand from a pdb file,but to use chimera command line,it has to load to many components,can you show me the pure source code to to this?thank you > > Hi, > I'm guessing your question means: "I have a bunch of PDB files that I need to remove the solvent and ligand from and therefore need to automate the process. How do I do that?". If that's not right, let me know. Anyway, the Chimera commands to remove solvent and ligand are: > > del solvent > del ligand > > and therefore in Python can be called by: > > from chimera import runCommand as rc > rc("del solvent") > rc("del ligand") > > > In Chimera's Programmer's Guide (http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html) there is a basic primer for looping through a bunch of data files and doing something on each one. You would just take the example in the basic primer and modify it to do the above (and write out the results). The direct link to the basic primer is here: > > http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > >

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Chimera-dev March 2014