• Make sure you have installed jre package
• Make sure you have installed 32bit compatible packages if the current linux is 64bit
• Download shiftx2 from http://www.shiftx2.ca/download.html
• Extract it

cd /home/usr/share
tar xvf ~/build/shiftx2/shiftx2-v104-linux-20110930.tgz
mv shiftx2-v104-linux-20110930/ shiftx2
cd shiftx2
make

* example (I've made a softlink for shiftx2_main.py as shiftx):

./shiftx2 -b '/home/yxue/work/test/*.pdb' -a BACKBONE -p 5.1 -t 300

原始输入文件为pdb文件，以1UBQ.pdb为例。

• Run the following command. 这一步会生成3个文件，分别是：1UBQ.cs，1UBQ.sxp，1UBQ.shifty.

shiftx2.py –i 1UBQ.pdb –e
# You can adjust temperature and pH by using option
# which can be shown by shiftx2.py -h

.

• 接下来需要运行老师已经写好的mkucsf.py文件，输入文件需要有1UBQ.pdb.cs和tpl.save，sim.save。（会生成sim.ucsf文件）
• 再用sparky打开sim.ucsf文件，进行一系列的调整，存为sim.save文件。