Difference between revisions of "Connect mode"

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(Created page with '= Overview = Sets how bonds are made when loading a file. Values: * 0 = distance-based and CONECT records * 1 = CONECT records * 2 = distance-based * 3 = (who knows, the code is…')
 
 
(12 intermediate revisions by 3 users not shown)
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Values:
 
Values:
* 0 = distance-based and CONECT records
+
* 0 = distance-based (excluding HETATM to HETATM) and CONECT records (default)
 
* 1 = CONECT records
 
* 1 = CONECT records
* 2 = distance-based
+
* 2 = distance-based, ignores CONECT records
* 3 = (who knows, the code is complicated)
+
* 3 = distance-based (including HETATM to HETATM) and CONECT records
 +
* 4 = for loading mmCIF: use the [http://www.wwpdb.org/data/ccd chemical components dictionary] to look up bonds (''in PyMOL 1.7.4, '''components.cif''' needs to be present in the current directory, later versions have a subset of the dictionary bundled with PyMOL, and look up unknown residues from a web service'')
  
 
= Syntax =
 
= Syntax =
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# ignore CONECT records
 
# ignore CONECT records
 
set connect_mode, 2
 
set connect_mode, 2
 +
# show current setting
 +
get connect_mode
  
 
</source>
 
</source>
  
 
= See Also =
 
= See Also =
 +
[[Load]], [[Connect_cutoff]], [[Connect_bonded]]
 +
 +
[[Category:Settings]]

Latest revision as of 15:08, 23 April 2018

Overview

Sets how bonds are made when loading a file.

Values:

  • 0 = distance-based (excluding HETATM to HETATM) and CONECT records (default)
  • 1 = CONECT records
  • 2 = distance-based, ignores CONECT records
  • 3 = distance-based (including HETATM to HETATM) and CONECT records
  • 4 = for loading mmCIF: use the chemical components dictionary to look up bonds (in PyMOL 1.7.4, components.cif needs to be present in the current directory, later versions have a subset of the dictionary bundled with PyMOL, and look up unknown residues from a web service)

Syntax

# ignore CONECT records
set connect_mode, 2
# show current setting
get connect_mode

See Also

Load, Connect_cutoff, Connect_bonded