Answers.Body: <p>my attempt :</p>
  <pre><code>import pymol
  
  from pymol.cgo import *
  
  from pymol import (
                      
                      cmd ,
                      )
  
  
  print('########## PYMOL VERSION ##########################################')
  print('         ',  cmd.get_version() )
  print('###################################################################')
  
  
  pymol.finish_launching()
  
  cmd.fetch('1tqn')
  
  cmd.remove('solvent')
  
  pos = cmd.get_position()
  
  r = 3
  
  print('###############################################################################\n')
  
  print('### POSITION : ' , pos,'  ###\n')
  
  print('###############################################################################\n')
  
  
  
  spherelist = [
      [COLOR,    1.000,    1.000,    0.000,
      SPHERE,   pos[0] , pos[1] , pos[2]  , r ],
  
      ]
  
  for i in spherelist:
      
      a = str(spherelist.index(i))
  
      cmd.load_cgo(i, 'sphere_'+a )
  
  
  cmd.zoom()
  
  cmd.set('cartoon_transparency' , '0.5')
  
  </code></pre>
  <p>result:</p>
  <p><a href="https://i.sstatic.net/Etqeo.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Etqeo.png" alt="enter image description here" /></a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-16T16:08:49.473Z
Answers.Text: Aaah, `load_cgo()` https://pymolwiki.org/index.php/Load_CGO ("Compiled Graphics Objects"). There are also other shapes: https://pymolwiki.org/index.php/CGO_Shapes. Thank you!
Answers.UserDisplayName: jhutar
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-16T10:20:28.550Z
Answers.LastActivityDate: 2023-10-16T10:20:28.550Z
Answers.UserDisplayName: pippo1980
Body: <p>I would like to add some 3D elements (balls and lines) to the PyMOL visualization to highlight some &quot;holes&quot; in the structure. Say I <code>fetch 1tqn</code> and I want to add a yellow ball somewhere (to specific coordinates, say <code>[-19, -23, -14]</code>) in the view. Or a bar from - to coordinates.</p>
  <p><a href="https://i.sstatic.net/1sSQv.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/1sSQv.png" alt="enter image description here" /></a></p>
  <p>I was going through wiki, did a online search but have not found a way how to add these simple 3D entities into the scene. I guess it should be trivial and I'm just using wrong queries. Because I need to add lots of these, I need to be able to do that via scripting interface.</p>
  <p>Thank you in advance for any help!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-16T08:59:40.483Z
Comments.Text: see here https://stackoverflow.com/questions/2060582/draw-a-colored-sphere-from-cartesian-coordinates-in-pymol/76749167#76749167 Draw a colored sphere from cartesian coordinates in pymol  and here https://pymolwiki.org/index.php/Load_CGO and https://pymolwiki.org/index.php/CGO_Shapes
Comments.UserDisplayName: pippo1980
Tags: <pymol><modelling><3d-structure>
Title: how to add a custom elements into PyMOL visualization?
ThreadText: # how to add a custom elements into PyMOL visualization?
  
  (Asked by: username_0 on 2023-10-15)
  
  I would like to add some 3D elements (balls and lines) to the PyMOL visualization to highlight some "holes" in the structure. Say I `fetch 1tqn` and I want to add a yellow ball somewhere (to specific coordinates, say `[-19, -23, -14]`) in the view. Or a bar from - to coordinates.
  
  [![enter image description here](https://i.sstatic.net/1sSQv.png)](https://i.sstatic.net/1sSQv.png)
  
  I was going through wiki, did a online search but have not found a way how to add these simple 3D entities into the scene. I guess it should be trivial and I'm just using wrong queries. Because I need to add lots of these, I need to be able to do that via scripting interface.
  
  Thank you in advance for any help!
  
  **Tags:** pymol, modelling, 3d-structure
  
  > **Comments:**
  > **username_1**: see here https://stackoverflow.com/questions/2060582/draw-a-colored-sphere-from-cartesian-coordinates-in-pymol/76749167#76749167 Draw a colored sphere from cartesian coordinates in pymol  and here https://pymolwiki.org/index.php/Load_CGO and https://pymolwiki.org/index.php/CGO_Shapes  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-10-16. Score: 2 | Accepted answer
  
  my attempt :
  
  ```
  import pymol
  
  from pymol.cgo import *
  
  from pymol import (
                      
                      cmd ,
                      )
  
  print('########## PYMOL VERSION ##########################################')
  print('         ',  cmd.get_version() )
  print('###################################################################')
  
  pymol.finish_launching()
  
  cmd.fetch('1tqn')
  
  cmd.remove('solvent')
  
  pos = cmd.get_position()
  
  r = 3
  
  print('###############################################################################\n')
  
  print('### POSITION : ' , pos,'  ###\n')
  
  print('###############################################################################\n')
  
  spherelist = [
      [COLOR,    1.000,    1.000,    0.000,
      SPHERE,   pos[0] , pos[1] , pos[2]  , r ],
  
      ]
  
  for i in spherelist:
      
      a = str(spherelist.index(i))
  
      cmd.load_cgo(i, 'sphere_'+a )
  
  cmd.zoom()
  
  cmd.set('cartoon_transparency' , '0.5')
  
  ```
  
  result:
  
  [![enter image description here](https://i.sstatic.net/Etqeo.png)](https://i.sstatic.net/Etqeo.png)
  
  > **Comments:**
  > **username_0**: Aaah, `load_cgo()` https://pymolwiki.org/index.php/Load_CGO ("Compiled Graphics Objects"). There are also other shapes: https://pymolwiki.org/index.php/CGO_Shapes. Thank you!  
  
  ---
  
  