February 2017 - Chimera-dev - RBVI Mailing Lists

Re: [chimera-dev] ChimeraX
by Tom Goddard 11 Apr '17

11 Apr '17

Hi Matt, There is some information about how to install Python packages with Chimera in the programming FAQ https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b but I believe Eric here said the suggested approach to doing pip install no longer works. A more hacky approach is to simply copy site-packages/Mido (or whatever the module is called) from your system installed version into the Chimera Python site-packages (in chimera/lib/python2.7/site-packages or Chimera.app/Contents/Resources/lib/python2.7/site-packages on Mac). Tom > On Jan 13, 2017, at 2:26 PM, Dougherty, Matthew T <matthewd(a)bcm.edu> wrote: > > I have looked around at python midi packages. > I think I can get around modifying the tk/qt event loops by polling the midi port. > > I did a pip install of 'Mido' on my Mac laptop for testing using the OSx python environment. > > To install the Mido library into chimera, what do you recommend? > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ================================================= > ================================================= > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Monday, November 21, 2016 12:53:04 PM > To: Dougherty, Matthew T > Cc: chimera-dev(a)cgl.ucsf.edu <mailto:chimera-dev@cgl.ucsf.edu> > Subject: Re: [chimera-dev] ChimeraX > > ***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe. > Hi Matt, > > The way to use MIDI in ChimeraX would be to include a MIDI / Qt5 library. Qt5 is the window toolkit used by ChimeraX and it controls the receiving of events from devices. I don’t know of an adequate Qt / MIDI library exists. Really we would want PyQt5 / MIDI since all Qt in ChimeraX is done in Python. The top Qt / MIDI hit is the QMidi library > > https://github.com/waddlesplash/QMidi <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_waddlesplas…> > > which apparently only handles output of MIDI events, and it sounds like you are primarily interested in input of MIDI events to ChimeraX. > > We welcome any recommendations on what PyQt library could handle incoming MIDI events. My quick web search turned up nothing. > > Tom > > > >> On Nov 18, 2016, at 9:47 AM, Dougherty, Matthew T wrote: >> >> Many of the USB devices I have been looking at for control surfaces are midi-centric, primarily coming out of the music industry. >> >> For simple devices, not going the midi-route is usually straight forward, although can get complex supporting cross-platform. >> >> For complex devices such as DS1, midi appears to be the best method for dial boxes. There is also economical advantages and an ongoing evolution of such devices. >> https://www.amazon.com/Livid-Instruments-Portable-Digital-Mixer/dp/B00M4OEW… <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.amazon.com_Livid-2…> >> >> It also allows one to take advantage of manufacturer software in configuring baseline operational conditions (setting dial colors, ranges, toggling action of buttons). >> >> >> We have talked about midi in the event loop before. At the time it was not clear how/if this could work under chimeraX. >> >> Any further ideas? >> >> >> >> >> Matthew Dougherty >> National Center for Macromolecular Imaging >> Baylor College of Medicine >> ================================================= >> ================================================= >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mail…>

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Send PDB and CCP4 selected to an external program
by Pablo Solar Rodríguez 27 Feb '17

27 Feb '17

Hello again dear mates! I've been working those days in my extension and the GUI es almost finished. Now I want to fill this skeleton with the process logic. To understand between us, I have an external compiled program that is executed in shell this way: ./bin/myProgram ./dir1/pdbselected.pdb ./dir/mapselected.ccp4 arg3 arg3 arg4 And for sure, in my .py test, it has to be executed as: import subprocess subprocess.call(["./Users/Solar/Desktop/parent/child1/child2/bin/myProgram", "/Users/Solar/Desktop/parent/child1/child2/dir1/pdbselected.pdb", "/Users/Solar/Desktop/parent/child1/child2/dir1/mapselected.ccp4", "arg3", "arg4", "arg5"]) The problem is to execute this in Chimera as an extension. The coding I made for the PDB and the Map it's similar to the FitMap tool (in Volume Data), where I use: ... # PDB from chimera import Molecule mlist = [m for m in fit_object_models() if isinstance(m, Molecule)] fstart = mlist[0] if mlist else None from chimera.widgets import ModelOptionMenu om = ModelOptionMenu(ff, labelpos = 'w', label_text = 'Fit ', initialitem = fstart, listFunc = fit_object_models, sortFunc = compare_fit_objects, command = self.object_chosen_cb) om.grid(row = 0, column = 0, sticky = 'w') self.object_menu = om # Map fm = Volume_Menu(ff, ' in map ') fm.frame.grid(row = 0, column = 1, sticky = 'w') self.map_menu = fm -- The question is, how can I pass the PDB to the compiled program as it is expected? Or, another possible solution, the paths of the PDB and the Map loaded in Chimera? I didn't found any friendly doc (methods, info and so on) about this and and I'm a mess :/ Thank you in advance dear coworkers! Pablo

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Register-Unregister Chimera Extension (Plugin) to check source code changes
by Pablo Solar Rodríguez 21 Feb '17

21 Feb '17

Hi all again, While I try how to debug my plugin with Chimera (I posted that question here), I downloaded the 'Fit in map' tool source code to create my own plugin from it. So I changed the name in ChimeraExtension.py and loaded it in Tools -> Volume Data to check that my new plugin was loaded succesfully. The point now is that when I make some changes in my code, they are not immediately visible when I open the plugin again. Even more, I am not capable to "reload" the plugin with the new changes. Any solution to this? As I told you before, I'm fully newbie with Chimera and I feel pretty lost Thank you in advance!

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Debugging own extension in Mac OS X
by Pablo Solar Rodríguez 21 Feb '17

21 Feb '17

Hello all, My name is Pablo Solar and I am newbie in a real BioInformatics work, specifically in Chimera. Due to my new project requirements, I want/need to write a Chimera Extensión which executes an existing tool for fitting maps in an exhaustive way. I started to read the documentation available and the programmers guide, but the fist question that came to my mind is about debugging. I would like to know how could I debug my extension python code while I work with Chimera at the same time. Is this possible? I mean, opening my extension in Chimera (Tools -> preferences and so on) and starting to debug the _init_py and the rest of my files. How should I configure my environment? What framework to use? That kind of things Thank you in advance. I think I will post questions frequently because, as I said, this is totally new to me. By the way, I suscribed to the mailing list with my personal mail (pablosolar.r(a)gmail.com) I would like to give you all kind regards and hope to learn from you as much as possible. Just need a bit of patience... :) Keep in touch and thank you in advance, Pablo Solar.

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Linking Chimera with Tetr
by Gordon Gibb 08 Feb '17

08 Feb '17

Dear developers, I have been working on integrating Tetr (a command line tool to construct/modify molecular systems for use in computational chemistry codes such as CASTEP and CP2K - http://nms.kcl.ac.uk/lev.kantorovitch/codes/lev00/index.html <http://nms.kcl.ac.uk/lev.kantorovitch/codes/lev00/index.html>) with Chimera. To do this we have written a plugin to Chimera that runs an instance of Tetr in a console, with the user being able to type commands into Tetr. The aim is to have Chimera visualise the system being constructed in Tetr, and to update the visualisation based to changes made in Tetr. At present whenever a command is send to Tetr (which in response to this command may re-write a file containing the molecular system), the plugin looks to see if this file has changed, and if so gets Chimera to reload this file and visualise it. As far as I can tell, there isn’t a ‘reload’ option in Chimera, so instead I close the model (saving its xform matrix first), then open the modified file, and set its xform matrix to restore the old viewing angle etc. For example: #save xform matrix and close model xf=model.openState.xform chimera.openModels.close(model) #open updated file into model number baseId chimera.openModels.open(filename,baseId=baseId) #retrieve model from the list of open models modlist=chimera.openModels.list() for mod in modlist: if mod.id == baseId: model=mod break #set the xform matrix model.openState.xform=xf What I was wondering was 1) if this is a sensible way to go about things, and 2) if there is a way to retrieve and store visualisation information such as displaying the molecule as ball and stick, wireframe etc such that this can be re-applied to the newly opened model, since at present any visualisation information is not retained when re-opening a file. Thanks in advance, Gordon ----------------------------------------------- Dr Gordon P S Gibb EPCC, The University of Edinburgh The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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(no subject)
by Kavya Shankar 02 Feb '17

02 Feb '17

Hi, Is it possible to find the distance between a point and a line in chimera? I am trying to find the distance from the center of mass of the protein to the 2 fold axis of the homodimer. Thanks. Regards, Kavya

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