[chimera-dev] ChimeraX

Tue Apr 11 10:32:58 PDT 2017

Go with preconfigured if that is what they recommend.  Use pip install as described in the January 13 message and see if it works.  I don’t know if the wheel includes the HDF5 libraries.  Chimera includes HDF5 libraries (version 1.8.9) in chimera/lib.  Maybe h5py will use these or include its own.

	Tom

> On Apr 10, 2017, at 5:32 PM, Dougherty, Matthew T <matthewd at bcm.edu> wrote:
> 
> Hi Tom,
> 
> I am planning to use the h5py library.
> 
> Referring to the email 1/13/17, I was wondering what would be the best route.
> 
> Looking at the h5py website:     http://docs.h5py.org/en/latest/build.html <http://docs.h5py.org/en/latest/build.html>
> 
> not sure if I should go with a preconfigured or the source install. pre-configured is what they recommend, I not making any changes for Mac, but not clear if I should do this for chimera.
> 
> 
> Looking at the download area, https://pypi.python.org/pypi/h5py/2.7.0 <https://pypi.python.org/pypi/h5py/2.7.0> 
> the python library is in whl format
> 
> 
> Matthew Dougherty
> National Center for Macromolecular Imaging
> Baylor College of Medicine
> =================================================
> =================================================
> From: Tom Goddard <goddard at sonic.net>
> Sent: Friday, January 13, 2017 8:38:56 PM
> To: Dougherty, Matthew T
> Cc: chimera-dev at cgl.ucsf.edu
> Subject: Re: [chimera-dev] ChimeraX
>  
> 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 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimera_docs_ProgrammersGuide_faq.html-23q3b&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=s5qAVmF9zmMDL9NYLkHBPGWH46D1Q7DG_mOEXbHpQ4w&s=h0s58KLyIgJOslR1p0LWNV4MNf5XxvgSXy72X8XFL10&e=>
> 
> 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 at bcm.edu <mailto:matthewd at 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 at sonic.net <mailto:goddard at sonic.net>>
>> Sent: Monday, November 21, 2016 12:53:04 PM
>> To: Dougherty, Matthew T
>> Cc: chimera-dev at cgl.ucsf.edu <mailto:chimera-dev at 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_waddlesplash_QMidi&d=DgMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=YSU301onuzBBah5qy89GRTNL5PhzKOjMx-HOYC8_sMQ&s=9_fN2otNCHI9eFtt4LSxl9b9nKrTFPjcRM6Gzi-8bsg&e=>
>> 
>> 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/B00M4OEWMW/ref=sr_1_1?ie=UTF8&qid=1479490715&sr=8-1&keywords=livid+ds1 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.amazon.com_Livid-2DInstruments-2DPortable-2DDigital-2DMixer_dp_B00M4OEWMW_ref-3Dsr-5F1-5F1-3Fie-3DUTF8-26qid-3D1479490715-26sr-3D8-2D1-26keywords-3Dlivid-2Bds1&d=DgMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=YSU301onuzBBah5qy89GRTNL5PhzKOjMx-HOYC8_sMQ&s=kwBeFxV6UE7XEm6Mrx9c5rzqHCfSaEjuTGoMCjd7VCI&e=>
>>> 
>>>  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
>>> =================================================
>>> =================================================
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