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 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 <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