在跟随其他大佬的帖子下载开源版pymol的时候,发现了anaconda版本和pymol版本不兼容的情况,最新的anaconda版本conda下载pymol-2.4.0-cp38-cp38-win_amd64.whl之后,显示出的pymol窗口是这样怪异的版本,命令窗口和图形窗口可以分开,看分子都是正常的,但是导出动画视频的编码器出现了问题(如下图3.、4)
找了很多帖子,补下载什么的都没用,最后在一个学术论坛上找到了答案,不过人家是用的miniconda的环境,我还是继续用的anaconda2023的环境,以此篇日志记录一下
详细下载过程是:进到你想下载pymol的文件夹,打开cmd或者powershell可以试一下
D:\XZY\RJ\Pymol>conda create -n python38 python=3.8 #下载好conda之后要创建python环境,创建了一个存放python环境的单位 ,名为python38
D:\XZY\RJ\Pymol>conda activate python38 #激活python环境,之后打开conda要使用python时都要激活一下
(python38)D:\XZY\RJ\Pymol>conda install -c conda-forge pymol-open-source #下载开源版pymol
(python38) D:\XZY\RJ\Pymol>conda install -c conda-forge ffmpeg #下载ffmpeg的插件
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 23.7.4
latest version: 23.11.0
Please update conda by running
$ conda update -n base -c defaults conda
Or to minimize the number of packages updated during conda update use
conda install conda=23.11.0
## Package Plan ##
environment location: D:\XZY\RJ\conda\envs\python38
added / updated specs:
- ffmpeg
The following packages will be downloaded:
package | build
---------------------------|-----------------
ffmpeg-4.3.1 | ha925a31_0 26.2 MB conda-forge
------------------------------------------------------------
Total: 26.2 MB
The following NEW packages will be INSTALLED:
ffmpeg conda-forge/win-64::ffmpeg-4.3.1-ha925a31_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(python38) D:\XZY\RJ\Pymol>conda install -c schrodinger mpeg_encode #另一个插件
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 23.7.4
latest version: 23.11.0
Please update conda by running
$ conda update -n base -c defaults conda
Or to minimize the number of packages updated during conda update use
conda install conda=23.11.0
## Package Plan ##
environment location: D:\XZY\RJ\conda\envs\python38
added / updated specs:
- mpeg_encode
The following packages will be downloaded:
package | build
---------------------------|-----------------
mpeg_encode-1 | 0 78 KB schrodinger
------------------------------------------------------------
Total: 78 KB
The following NEW packages will be INSTALLED:
mpeg_encode schrodinger/win-64::mpeg_encode-1-0
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2023.11.~ --> pkgs/main::ca-certificates-2023.12.12-haa95532_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(python38) D:\XZY\RJ\Pymol>conda install numpy
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 23.7.4
latest version: 23.11.0
Please update conda by running
$ conda update -n base -c defaults conda
Or to minimize the number of packages updated during conda update use
conda install conda=23.11.0
# All requested packages already installed.
(python38) D:\XZY\RJ\Pymol>pip install numpy #检查一下numpy组件有无安装,pip install和conda install 都可以试一下,虽然我不知道区别
Requirement already satisfied: numpy in d:\xzy\rj\conda\envs\python38\lib\site-packages (1.24.3)
(python38) D:\XZY\RJ\Pymol>pip install mkl #检查mkl有无安装
Requirement already satisfied: mkl in d:\xzy\rj\conda\envs\python38\lib\site-packages (2024.0.0)
Requirement already satisfied: intel-openmp==2024.* in d:\xzy\rj\conda\envs\python38\lib\site-packages (from mkl) (2024.0.2)
Requirement already satisfied: tbb==2021.* in d:\xzy\rj\conda\envs\python38\lib\site-packages (from mkl) (2021.11.0)
(python38) D:\XZY\RJ\Pymol> python -m pip install pmw #检查pmw有无安装,这三个组件对于pymol来说是必装的,如果要导出动画,那么上面的ffmpeg也要检查安装
Requirement already satisfied: pmw in d:\xzy\rj\conda\envs\python38\lib\site-packages (2.0.1)
至此,无法导出动画的问题就已解决,可能还是和安装方法有一定关系,我对象不是用的conda环境安装,那个方法就好像会给他把所有组件都装上了,就没有出现ffmpeg编码器不在的情况。
最后,如果需要创建Pymol的快捷打开方式,是在你安装anaconda的文件夹下-envs-python38-scripts-pymol.exe,我之前喜欢直接在conda的文件夹底下下载Pymol,那他就在canda的scripts能找到