pymol安装

最新推荐文章于 2024-07-24 14:41:11 发布

wlzhang123

最新推荐文章于 2024-07-24 14:41:11 发布

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文章标签： pymol

事情经常变化，首先参考

https://pymolwiki.org/index.php/Windows_Install

Open-Source PyMOL is available free of charge. It also allows sponsors to create highly customized PyMOL installations which might not be possible with the MSI installer.

这里就不涉及了。

Pre-compiled Open-Source PyMOL is available free from Christoph Gohlke of the Laboratory for Fluorescence Dynamics, University of California, Irvine

这个是目前比较流行的安装方式。

Install Python 2.7 for Windows (e.g., by going to http://www.python.org/downloads/). Use the standard options (which should mean that the installation directory is C:\Python27). It may be useful if C:\Python27 is listed in your system PATH variable.
Download the appropriate wheel files, along with all requirement wheel files (including pip, Numpy and PMW) into a single file directory, e.g., C:\PyMOL_installation

3.From this installation directory (to get there you can run

cd C:\PyMOL_installation

from the command prompt), run:

C:\Python27\python.exe pip-6.x.x-py2.py3-none-any.whl/pip install --no-index --find-links="%CD%" pymol_launcher

if C:\Python27 is part of your PATH variable, then running (where x refers to the version number of pip):

python pip-6.x.x-py2.py3-none-any.whl/pip install --no-index --find-links="%CD%" pymol_launcher

python pip-6.x.x-py2.py3-none-any.whl/pip install --no-index --find-links="%CD%" pymol_launcher-2.1-XXXXX

should suffice. To update PyMOL update the files in the PyMOL install directory and run:

pip install --upgrade --no-deps pymol.whl

where pymol.whl is replaced by the PyMOL wheel file name (not the launcher, the launcher should not require updating).

E:\Anaconda3\Lib\site-packages\

有pymol，pymol2，pmw。

E:\Anaconda3下有：

PyMOL.exe

问题就是：高版本的pse，在低版本打不开。

pip uninstall pymol-launcher-2.1

pip uninstall pmol

pip uninstall pmw

版本3的有点问题，后来还是装版本2的了。启动没有问题。但是由于之前有一个PyMOL.exe。

所以启动的时候会不太爽。修改为Pymol2.exe。就可以了。

Extend PyMOL with additional scripts

If you now want to extend the capabilities of PyMOL, and take advantage of all the available plugins+scripts "out there", then do the following.

First install "numpy" as an available module to Python. Select appropriate installer from here
Download the script/plugin collection Pymol-script-repo from a .zip file from here

git clone https://github.com/Pymol-Scripts/Pymol-script-repo

Unpack it to here: C:\Python27\Lib\site-packages\pymol\pymol_path\Pymol-script-repo Double check that the folder name is correct and the same.

Open "Notepad" and write.

# Add paths to sys.path so PyMOL can find modules and scripts
import sys, os
pymol_git = os.path.abspath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])

# Make setting changes to Plugin Manager
import pymol.plugins
pymol.plugins.preferences = {'instantsave': False, 'verbose': False}
pymol.plugins.autoload = {'apbs_tools': False}
pymol.plugins.set_startup_path([os.path.join(pymol_git, 'plugins'), os.path.join(sys.prefix, 'Lib', 'site-packages', 'pmg_tk', 'startup')])
pymol.plugins.preferences = {'instantsave': True, 'verbose': False}

Then "File->Save as->All files-> C:\Python27\Lib\site-packages\pymol\pymol_path\run_on_startup.py

Now start pymol, and enjoy all the plugins available from the menu.

PyMOL shortcut
Make a pymol directory in your homepath. mkdir %HOMEPATH%\pymol Then make sure, PyMOL starts here, when you open the shortcut.
Make a shortcut to the .cmd file, and modify it.
Target: C:\python27\PyMOL\pymol.cmd
Start in: %HOMEPATH%\pymol

补充open with设置：

https://zhidao.baidu.com/question/560798557697418844.html

1.打开注册表。开始运行输入regedit回车

2.像找文件夹一样打开路径：

HEKY_CURRENT_USER＼Software＼Microsoft＼Windows＼CurrentVersion＼Explorer＼FileExts

3.该路径下会出现所有的文件后缀文件夹，这里我找到.mp3

4.打开该路径下的OpenWithList

5.这时就会看到右边列出了许多打开的程序了，想用什么工具 你就以葫芦画瓢 就添加进去吧

 想加几个加几个 想不要那个 就不要那个！

6.关闭注册表即可。

但是还是直接改名比较方便。