Pdb use ter records: Difference between revisions
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When a molecule (e.g. a protein molecule) is saved in pdb format by PyMOL, a line of [http://www.wwpdb.org/documentation/format33/sect9.html#TER TER] record is inserted wherever the residue id is not sequential. To suppress this feature, set <tt>pdb_use_ter_records</tt> value to 0 before saving protein molecules. | When a molecule (e.g. a protein molecule) is saved in pdb format by PyMOL, a line of [http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#TER TER] record is inserted wherever the residue id is not sequential. To suppress this feature, set <tt>pdb_use_ter_records</tt> value to 0 before saving protein molecules. | ||
=Example= | == Version History == | ||
* 2.3.0 new implementation, [https://github.com/schrodinger/pymol-testing/commit/82440d760b6b2b48b2cb1ca6c0bb5347870a4541 works correctly with gaps] | |||
* 1.8.4 feature removed | |||
* <= 1.8.2 feature broken for various use cases (e.g. gaps) | |||
* <= 1.5.0.4 feature broken for HETATM polymer residues (e.g. MSE) | |||
== Example == | |||
<source lang="python"> | <source lang="python"> | ||
get pdb_use_ter_records # return current value of pdb_use_ter_records | get pdb_use_ter_records # return current value of pdb_use_ter_records | ||
set pdb_use_ter_records, 0 | set pdb_use_ter_records, 0 | ||
</source> | |||
== PyMOL API == | |||
cmd.set( | <source lang="python"> | ||
cmd.set('pdb_use_ter_records', 0) | |||
</source> | </source> | ||
== See Also == | |||
* [[pdb_conect_nodup]] | |||
* [[pdb_conect_all]] | |||
[[Category:Settings|Pdb_use_ter_records]] | |||
Latest revision as of 07:32, 17 December 2018
When a molecule (e.g. a protein molecule) is saved in pdb format by PyMOL, a line of TER record is inserted wherever the residue id is not sequential. To suppress this feature, set pdb_use_ter_records value to 0 before saving protein molecules.
Version History
- 2.3.0 new implementation, works correctly with gaps
- 1.8.4 feature removed
- <= 1.8.2 feature broken for various use cases (e.g. gaps)
- <= 1.5.0.4 feature broken for HETATM polymer residues (e.g. MSE)
Example
get pdb_use_ter_records # return current value of pdb_use_ter_records
set pdb_use_ter_records, 0
PyMOL API
cmd.set('pdb_use_ter_records', 0)