Molecular Sculpting - Revision history

Cchem: 1 revision

2018-11-12T04:22:57Z

1 revision

Speleo3: sculpt_field_mask

2018-10-19T14:41:39Z

sculpt_field_mask

Cchem: 6 revisions

2018-05-29T19:27:24Z

6 revisions

Hongbo zhu: put the source of the answer to the beginning.

2018-05-17T11:25:07Z

put the source of the answer to the beginning.

Pyadmin: 1 revision

2014-03-28T02:16:32Z

1 revision

OsvaldoMartin: /* See Also */

2013-10-17T11:26:07Z

Hongbo zhu: add reference to this entry

2013-10-10T11:45:28Z

add reference to this entry

Orbeckst: /* What the heck is molecular sculpting? */ reformatted

2011-04-28T17:11:26Z

What the heck is molecular sculpting?: reformatted

New page

==What the heck is molecular sculpting?==

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:

# Load a PDB file.
# Configure the mouse for editing (''Mouse'' menu) or click in the mouse/key matrix box.
# Select ''Sculpting'' from the ''Wizard'' menu. (or: Select ''auto-sculpting'' from the ''Sculpting'' 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.
# 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.

[[Category:Modeling_and_Editing_Structures|Molecular Sculpting]]

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 ==See Also==
-[[Optimize]]
+* [[sculpt_field_mask]] setting
 [[Category:Modeling_and_Editing_Structures|Molecular Sculpting]]

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 ==What the heck is molecular sculpting?==
 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.
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 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==
 [[Optimize]]

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 ==See Also==
 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 ]
 [[Category:Modeling_and_Editing_Structures|Molecular Sculpting]]

← Older revision		Revision as of 11:45, 10 October 2013
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	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.

		+	==See Also==
		+	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 ]

	[[Category:Modeling_and_Editing_Structures\|Molecular Sculpting]]		[[Category:Modeling_and_Editing_Structures\|Molecular Sculpting]]

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← Older revision	Revision as of 19:27, 29 May 2018
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