[Chimera-users] using scipy with Chimera

Tom Goddard goddard at sonic.net
Sat Jul 16 11:14:26 PDT 2016


Hi XBL,

  Unfortunately numpy 1.11 did not work in Chimera and I had to go back to using numpy 1.7 in the Chimera daily build because a molecular mechanics package we rely on, MMTK, won't work with numpy newer than 1.8.  The developer of MMTK, Konrad Hinsen, said it is too much work to update MMTK, so we are stuck using old numpy for now.  Our next generation ChimeraX program that will be available later this year (with limited functionality) will of course use the current numpy version (and not use MMTK).

	Tom



> On Jul 13, 2016, at 11:15 AM, Tom Goddard wrote:
> 
> Hi XBL,
> 
>  Ok I’ve updated the Chimera daily build to use numpy 1.11.1.  Will be available around 6 AM Pacific time tomorrow from the Chimera download page if he builds succeed.  I did not update the Chimera 1.11 release candidate because we expect to make that an official release in a week and that is too little time to be sure the new numpy works.
> 
> 	Tom
> 
> 
>> On Jul 12, 2016, at 3:17 PM, Xiao-Bo Li wrote:
>> 
>> Hi,
>> 
>> I need to use scipy with Chimera.  I like to copy over the scipy folder from my ubuntu's "/usr/lib/python2.7/dist-packages/scipy" directory.  This is what I have done in the past, and it works fine.
>> 
>> However, when i installed the .bin file for Chimera from Chimera's website (I tried versions 1.11 and 1.8.1), I find that the numpy versions there are 1.7.0b2.  The numpy version on my ubuntu computer is 1.11.0.
>> 
>> Since my ubuntu python's numpy, and Chimera's numpy are different versions, I can no longer using the scipy folder for Chimera.  Can you please update Chimera's numpy version to 1.11.0?
>> 
>> XBL
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