[[ http://www.shiftx2.ca/ | SHIFTX2 ]]
====== shiftx2 ======
===== Installation =====
  * 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
<code>
cd /home/usr/share
tar xvf ~/build/shiftx2/shiftx2-v104-linux-20110930.tgz
mv shiftx2-v104-linux-20110930/ shiftx2
cd shiftx2
make
</code>
===== shiftxp =====
 * example (I've made a softlink for shiftx2_main.py as shiftx):
<code>
./shiftx2 -b '/home/yxue/work/test/*.pdb' -a BACKBONE -p 5.1 -t 300
</code>

===== Procedure by Ge HAN =====
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.
<code>
shiftx2.py –i 1UBQ.pdb –e
# You can adjust temperature and pH by using option
# which can be shown by shiftx2.py -h
</code>.
  * 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。