Difference between revisions of "Pdb use ter records"

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(add see also (Pdb_conect_nodup and Pdb_Conect_All) put the PyMOL api example under the title "PyMOL API")
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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/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.
 
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
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</source>
 
</source>
  
===PYMOL API===
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== PyMOL API ==
 
<source lang="python">
 
<source lang="python">
 
cmd.set('pdb_use_ter_records', 0)
 
cmd.set('pdb_use_ter_records', 0)
 
</source>
 
</source>
  
===SEE ALSO===
+
== See Also ==
[[Pdb_conect_nodup]], [[Pdb_Conect_All]]
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 +
* [[pdb_conect_nodup]]
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* [[pdb_conect_all]]
  
 
[[Category:Settings|Pdb_use_ter_records]]
 
[[Category:Settings|Pdb_use_ter_records]]

Latest revision as of 08:32, 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)

See Also