Difference between revisions of "Connect mode"
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Cowsandmilk (talk | contribs) (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…') |
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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 = ( | + | * 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 = | ||
| Line 12: | Line 13: | ||
# 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