Change molecular representation

README.md

@@ -53,12 +53,7 @@ git clone https://git.mki.or.id/coredev/cmmde
 ```bash
 cd cmmde
 ```
-3. Install the code:
-```bash
-chmod +x install.sh
-./install.sh
-```
-4. Jika ditemukan _error_:
+3. Jika ditemukan _error_:
 ```bash
 FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/pip3.9'
 ```
@@ -66,3 +61,14 @@ Lakukan:
 ```bash
 ln -s /usr/bin/pip /usr/bin/pip3.9
 ```
+4. Jika ingin menjalankan program cmmde-gui:
+```bash
+cd cmmde_gui
+panel serve gui.py --autoreload
+```
+
+## Catatan
+Jika hanya ingin menginstall CMMDE versi _text-based_, cukup lakukan langkah 1-3. Langkah 4 hanya dilakukan jika ingin menjalankan CMMDE versi _graphical user interface_. Namun versi ini perlu menginstall `panel-chemistry versi 0.0.11`.
+```bash
+ pip install -Iv panel-chemistry==0.0.11
+```

cmmde_gui/gui.py

@@ -280,7 +280,7 @@ def cmmde_gui():
         with open('cmmd.xyz','r') as f:
             xyz = f.read()
         xyzview.addModel(xyz,'xyz')
-        xyzview.setStyle('stick')
+        xyzview.setStyle({'stick':{},'sphere':{'scale':.30}},viewer=(0,0))
         xyzview.zoomTo()
         xyzviewer.object = xyzview
         

install.sh

@@ -1,4 +1,5 @@
 # Install the requirements
+sudo apt install python3-pip
 pip install ase pymatgen gmxscript prettytable acpype MDAnalysis statsmodels
 ## Aktifkan dua baris di bawah jika anda ingin menginstall cmmde-gui.  
 #pip install -Iv panel-chemistry==0.0.11