January 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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midi
by Dougherty, Matthew T 30 Jan '17

30 Jan '17

Hi, I got the midi interface working with chimera, thanks. I ended up using the rtmidi package instead of mido. https://pypi.python.org/pypi/python-rtmidi Midi will significantly reduce my reliance on accelerators. It will give me the ability to pass multivariate parameters from hardware and modify LED displays on those devices. Previous efforts directly working with USB has be difficult because of lack of compliance and limited open source methods. The software I developed allows the DS1 control surface to easily control volume rendering and stereographics. http://lividinstruments.com/products/ds1/ I am anticipating this will improve operational viz for tomograms. If users demonstrate value in device, will release as an chimera extension. Internal NCMI testing begins next week. Also looking at other inexpensive midi devices. Recommending chimera ship with rtmidi library. thanks, Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Automate Energy Minimization of pdb files
by Ajay Pal 20 Jan '17

20 Jan '17

Dear Developers I am trying to build a chimera integrated python script to energy minimize protein pdb files. I have a list of ~400 pdb files (clean homology models) which I need to Energy minimize Can you please help me with this matter: like how to select files from directory adding H-atoms selecting the forcefield, etc how can I automate this whole process ? Thank you, I would appreciate all your help. Ajay -- Ajay Pal PhD Research Student Dublin Institute of Technology, Dublin -- This email originated from DIT. If you received this email in error, please delete it from your system. Please note that if you are not the named addressee, disclosing, copying, distributing or taking any action based on the contents of this email or attachments is prohibited. www.dit.ie Is ó ITBÁC a tháinig an ríomhphost seo. Má fuair tú an ríomhphost seo trí earráid, scrios de do chóras é le do thoil. Tabhair ar aird, mura tú an seolaí ainmnithe, go bhfuil dianchosc ar aon nochtadh, aon chóipeáil, aon dáileadh nó ar aon ghníomh a dhéanfar bunaithe ar an ábhar atá sa ríomhphost nó sna hiatáin seo. www.dit.ie Tá ITBÁC ag aistriú go Gráinseach Ghormáin – DIT is on the move to Grangegorman <http://www.dit.ie/grangegorman>

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chimerax and write pdb files question
by Wolfgang Lugmayr 18 Jan '17

18 Jan '17

dear chimerax developers, i found out, that you skipped writing pdb files and use only mmcif/pdbx. i need to write the selected structures as pdb for the usage with the rosetta modeling software. in chimera1 i used your save as dialog for this. are you (or somebody else) planning to also implement a pdb file writer for chimerax? cheers, wolfgang -- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Institute of Molecular Biotechnology (IMBA) Dr. Bohr-Gasse 3-7 (Room 6.14) 1030 Vienna, Austria Tel.: +43 (1) 790 44-4649 Email: w.lugmayr(a)uke.de http://www.cssb-hamburg.de/ -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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opening file in extension.
by Devin Haslam 13 Jan '17

13 Jan '17

I am developing an extension for the newest version of chimera. At the moment, my extension takes several .pdb files as input and opens them in the viewer. Currently, I am using the chimera.openmodels.open() to display these pdb files. This was not a problem until I started using .pdb files that consisted of hundreds of points. Because I am opening multiple .pdb files, the call to "setCategory()" does not execute fast enough and the root will have changed. In summary, what will I have to do in code to open multiple .pdb files made up of hundreds of points? -- Devin Haslam Old Dominion University, Norfolk, Virginia

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chimerax - registering an external tool problem
by Wolfgang Lugmayr 11 Jan '17

11 Jan '17

dear chimera developers, i'm currently porting one of our chimera 1.x plugins called starmap to chimerax. basic questions: 1. should the package be e.g. chimerax-starmap or just starmap? 2. is there a recommended way when i should upload to the toolshed repository? my current problem: i use chimerax's python3.5 pip to install and remove my tests. my test package is called chimerax.starmapx (+.__init.py__) i had a look at your toolshed and added test categories like follows to the metadata (installed version): Classifier: ChimeraX :: Bundle :: Volume data :: 1,1 :: chimerax.starmap :: chimerax.starmap :: Classifier: ChimeraX :: Tool :: StarMapX :: Volume data :: Run Rosetta refinements Classifier: ChimeraX :: Command :: apix :: Volume data :: Run Rosetta apix Requires-Dist: ChimeraX-Core (>=0.1) Requires-Dist: pyparsing i also used "General" instead of "Volume data" for debugging. i have overriden the BundleAPI get_class, start_tools, register_command similar to blastprotein. unfortunatly my test plugin never shows up in chimerax (e.g. ts list) and the command "stm apix" is not registered. i debugged the toolshed (standalone - not in chimerax) and if i print the contents of line 720 - end of_load_bundle_infos() i get ...using SteamVR]], ChimeraX-StarMap (installed) [version: 0.1.2] [api package: chimerax.starmap] [category: Volume data] [tool: StarMap [categories: Volume data] [synopsis: Run Rosetta refinements]] [command: apix [categories: Volume data] [synopsis: Run Rosetta refinements]], ChimeraX-Stringdb (installed) [version: 0.1]... and a little bit before ('checking', <InstalledDistribution 'ChimeraX-StarMap' 0.1.2 at '/projects/marlovits/lugmayr/workspace/ChimeraX/lib/python3.5/site-packages/ChimeraX_StarMap-0.1.2.dist-info'>) do i miss something during the registration process? cheers, wolfgang --- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Institute of Molecular Biotechnology (IMBA) Dr. Bohr-Gasse 3-7 (Room 6.14) 1030 Vienna, Austria Tel.: +43 (1) 790 44-4649 Email: w.lugmayr(a)uke.de http://www.cssb-hamburg.de/ -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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ChimeraX on Centos7
by Wolfgang Lugmayr 02 Jan '17

02 Jan '17

dear chimera users, if you want to test/use the daily releases of chimerax on centos7 and have an error like ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /opt/chimerax/0.1-daily/lib/python3.5/site-packages/chimerax/core/geometry/_geometry.so) you might find the following link useful: http://www.marlovitslab.org/chimerax/ the provided libraries could also work on other linux distributions, so just try. cheers, wolfgang -- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Institute of Molecular Biotechnology (IMBA) Dr. Bohr-Gasse 3-7 (Room 6.14) 1030 Vienna, Austria Tel.: +43 (1) 790 44-4649 Email: w.lugmayr(a)uke.de http://www.cssb-hamburg.de/ -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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Chimera-dev January 2017