Difference between revisions of "Pdb use ter records"

From PyMOLWiki
Jump to: navigation, search
(fix broken link to PDB page (ter format) and add this page to the settings page)
(add see also (Pdb_conect_nodup and Pdb_Conect_All) put the PyMOL api example under the title "PyMOL API")
Line 1: Line 1:
 
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=  
+
===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>
  
import cmd
+
===PYMOL API===
cmd.set(name='pdb_use_ter_records', value=0) # same effect
+
<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]]
 
[[Category:Settings|Pdb_use_ter_records]]

Revision as of 18:26, 15 September 2015

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.

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

Pdb_conect_nodup, Pdb_Conect_All