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/

—Eric


Eric Pettersen
UCSF Computer Graphics Lab



On Aug 20, 2019, at 10:32 PM, William <3121437640@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@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@qq.com>; 
抄送: "chimera-users"<chimera-users@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.  Question 3b.  If those instructions don’t work, please let us know.

—Eric

Eric Pettersen
UCSF Computer Graphics Lab