[Chimera-users] scipy problem

Eric Pettersen pett at cgl.ucsf.edu
Thu Aug 22 17:01:28 PDT 2019

Yes, MMTK — which we use under the hood for minimization, computing MD trajectories, and a few other things — will not work with numpy 1.9 or newer.  This is obviously a problem for installing an up-to-date scipy.  You never really said what your overall goal was that required scipy, but maybe you could use PyChimera?   https://pychimera.readthedocs.io/en/latest/ <https://pychimera.readthedocs.io/en/latest/>


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Aug 20, 2019, at 10:32 PM, William <3121437640 at qq.com> wrote:
> Dear Eric,
>        I have tried the instructions following the FAQ, but there is another problem. The scipy installed successfully. However, it installed a higher version of the numpy when installing scipy. And the older version of numpy is still in. The chimera can not work. Anyway, thanks a lot.
> ------------------ 原始邮件 ------------------
> 发件人: "Eric Pettersen"<pett at cgl.ucsf.edu>; 
> 发送时间: 2019年8月20日(星期二) 凌晨1:46
> 收件人: "William"<3121437640 at qq.com>; 
> 抄送: "chimera-users"<chimera-users at cgl.ucsf.edu>; 
> 主题: Re: [Chimera-users] scipy problem
> Hi William,
> 	I don’t know why Jaime’s instructions don’t work.  Maybe he can follow up.  Regardless, we have our own instructions for installing pip (and pip-able packages like scipy).  It’s in the Chimera Programming FAQ <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html>.  Question 3b.  If those instructions don’t work, please let us know.
> —Eric
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab

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