Difference between revisions of "Molecular Sculpting"

From PyMOLWiki
Jump to: navigation, search
(sculpt_field_mask)
 
(5 intermediate revisions by 4 users not shown)
Line 1: Line 1:
 
==What the heck is molecular sculpting?==
 
==What the heck is molecular sculpting?==
  
 +
Warren DeLano's reply to the question "molecular sculpting" in PyMOL mailing list.[http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00359.html ]:
 +
 +
<blockquote>
 
Molecular sculpting works like a real-time energy minimizer, except that it isn't minimizing the energy. Instead, its just trying to return local atomic geometries (bonds, angles, chirality, planarity) to the configuration the molecules possess when they were first loaded into PyMOL.
 
Molecular sculpting works like a real-time energy minimizer, except that it isn't minimizing the energy. Instead, its just trying to return local atomic geometries (bonds, angles, chirality, planarity) to the configuration the molecules possess when they were first loaded into PyMOL.
  
 
To actually use this feature:
 
To actually use this feature:
  
  1. Load a PDB file.
+
# Load a PDB file.
  2. Configure the mouse for editing (Mouse menu) or click in the mouse/key matrix box.
+
# Configure the mouse for editing (''Mouse'' menu) or click in the mouse/key matrix box.
  3. Select "auto-sculpting" from the Sculpting menu.
+
# Select ''Sculpting'' from the ''Wizard'' menu. (or: Select ''auto-sculpting'' from the ''Sculpting'' menu.)
  4. Select Sculpting from the Wizard menu.
+
# ''Ctrl-middle-click'' on any atom in your protein to activate sculpting. The green part will be free to move. The cyan part will be a fixed cushion to provide context. The grey part will be excluded.
  5. Ctrl-middle-click on any atom in your protein to activate sculpting
+
# Now perform any conformational editing operation in the green region such as:
      the green part will be free to move
+
#* ''ctrl-left-click-and-drag'' on an atom
      the cyan part will be a fixed cushion to provide context
+
#* ''ctrl-right-click'' on a bond, then ''ctrl-left-click-and-drag'' about that bond.
      the grey part will be excluded.
 
  6. Now perform any conformational editing operation in the green region such as:
 
      ctrl-left-click-and-drag on an atom
 
      ctrl-right-click on a bond, then ctrl-left-click-and-drag about that bond.
 
  
 
You can adjust the radius and cushion using the blue pop-up menus.
 
You can adjust the radius and cushion using the blue pop-up menus.
  
 
Right now I'm not sure the sculpting feature is more than entertainment, but my expectation is that it will become part of PyMOL's crystallographic model building system in the future.
 
Right now I'm not sure the sculpting feature is more than entertainment, but my expectation is that it will become part of PyMOL's crystallographic model building system in the future.
 +
</blockquote>
 +
 +
==See Also==
 +
 +
* [[sculpt_field_mask]] setting
 +
* [[Optimize]] plugin
  
  
[[Category:Category:Modeling_and_Editing_Structures|Molecular Sculpting]]
+
[[Category:Modeling_and_Editing_Structures|Molecular Sculpting]]

Latest revision as of 10:41, 19 October 2018

What the heck is molecular sculpting?

Warren DeLano's reply to the question "molecular sculpting" in PyMOL mailing list.[1]:

Molecular sculpting works like a real-time energy minimizer, except that it isn't minimizing the energy. Instead, its just trying to return local atomic geometries (bonds, angles, chirality, planarity) to the configuration the molecules possess when they were first loaded into PyMOL.

To actually use this feature:

  1. Load a PDB file.
  2. Configure the mouse for editing (Mouse menu) or click in the mouse/key matrix box.
  3. Select Sculpting from the Wizard menu. (or: Select auto-sculpting from the Sculpting menu.)
  4. Ctrl-middle-click on any atom in your protein to activate sculpting. The green part will be free to move. The cyan part will be a fixed cushion to provide context. The grey part will be excluded.
  5. Now perform any conformational editing operation in the green region such as:
    • ctrl-left-click-and-drag on an atom
    • ctrl-right-click on a bond, then ctrl-left-click-and-drag about that bond.

You can adjust the radius and cushion using the blue pop-up menus.

Right now I'm not sure the sculpting feature is more than entertainment, but my expectation is that it will become part of PyMOL's crystallographic model building system in the future.

See Also