mod gui and readme

cmmde_gui/gui.py

@@ -260,6 +260,7 @@ def cmmde_gui():
             xyz = f.read()
         xyzview.addModel(xyz,'xyz')
         xyzview.setStyle('stick')
+        xyzview.zoomTo()
         xyzviewer.object = xyzview
         
 

install.sh

@@ -1,5 +1,8 @@
 # Install the requirements
 pip install ase pymatgen gmxscript prettytable acpype MDAnalysis
+## Aktifkan dua baris di bawah jika anda ingin menginstall cmmde-gui.  
+#pip install -Iv panel-chemistry==0.0.11
+#pip install -Iv jinja2==3.0.1
 sudo apt install -y cmake 
 sudo apt install -y libblas-dev
 sudo apt install -y libarpack2-dev
@@ -11,8 +14,21 @@ echo "export PYTHONPATH=`pwd`/lib:$PYTHONPATH" >> ~/.bashrc
 echo "export PATH=`pwd`/bin:$PATH" >> ~/.bashrc
 echo "export ORCA_COMMAND=/opt/orca/orca" >> ~/.bashrc
 echo "export XTB_COMMAND=/usr/local/bin/xtb" >> ~/.bashrc
-# PATH to DCDFTBMD program, please refer the README.md to register the program at Nakai Lab of Waseda University
+## PATH to DCDFTBMD program, please refer the README.md to register the program at Nakai Lab of Waseda University
+## Aktifkan baris di bawah jika anda sudah menginstall DCDFTBMD
 #echo "export DCDFTB_COMMAND=/path/to/DCDFTBMD/bin/binary" >> ~/.bashrc
 # If you have GROMACS
 #echo "export GROMACS_COMMAND=`pwd`/lib/cmmde_solution.py" >> ~/.bashrc
+#echo "export GROMACS_DIR=/path/to/gromacs/build/bin" >> ~/.bashrc
+#echo "alias gmx='path/to/gromacs/bin/gmx'" >> ~/.bashrc
+#echo "export GROMACS_FF=/path/to/gromacs/source/share/top"
+#echo "export AMBER_FF=/path/to/miniconda/dat/leap/cmd"
+#echo "export DFTB_COMMAND=/path/to/dftb+/bin/dftb+"
+#echo "export DPTOOLS_DIR=/path/to/dftbplus/tools/dptools/bin"
+# If you have DOCK6
+#echo "export DMS_COMMAND=/usr/local/bin/dms" >> ~/.bashrc
+#echo "export DOCK_DIR=/path/to/dock6/bin" >> ~/.bashrc
+#echo "export DOCK_PARM=/path/to/dock6/parameters" >> ~/.bashrc
+
+## Pada kasus-kasus tertentu, source ~/.bashrc akan perlu dilakukan secara manual jika cmmde.py tidak terdeteksi di $PATH
 source ~/.bashrc