Save sep

Description

Saves all objects as separate PDB files. Useful if you want to do things like combine separate *.pse files.

Code

from pymol import cmd
import glob
import re

def save_sep(prefix=''):
  """
  save_sep <prefix>

  saves multiple objects into multiple files using an optional prefix name.

  e.g. save_sep prefix
  """
  obj_list = cmd.get_names('models')

  if obj_list:
    for i in range(len(obj_list)):
#      if ( obj == '' ):
      obj_name = "%s%s.pdb" % (prefix, obj_list[i])
      cmd.save(obj_name, obj_list[i])
      print "Saving %s" %  obj_name
  else:
    print "No objects found"
    
cmd.extend('save_sep',save_sep)

	PyMOL Script Library
Running Scripts	Script Requests	Policy
Structural Biology	Objects and Selections	Math/Geometry/CGO
AAindex AngleBetweenHelices Angle between domains AutoMultiFit Average b BbPlane BiologicalUnit BiologicalUnit/Quat Bondpack Cart to frac Ccp4 contact Ccp4 ncont Ccp4 pisa Centroid ColorByRMSD Color By Mutations Color by conservation Colorblindfriendly Colorbydisplacement Consistent View/ Map Inspect Contact Surface CreateSecondaryStructure Cyspka Displacementmap DistancesRH Draw Protein Dimensions Dssp Dssr block DynoPlot Elbow angle FindSurfaceResidues Helicity check HighlightAlignedSS InterfaceResidues Intra xfit Iterate sses LigAlign Load aln Load new B-factors Mcsalign Measure Distance Motif Msms surface Nmr cnstr PDB plugin Pairwise distances Propka Resicolor plugin Ribosome PyMOL Plugin RmsdByResidue Rotamer Toggle RotationAxis ShowLigandWaters Show contacts Sidechaincenters Ss Sst Transformations Translate And Measure WriteSS Xfit	AlphaToAll Annotate v Cluster Count CollapseSel Color Objects ConnectedCloud Count molecules in selection DistancesRH Expand To Surface FindObjectsNearby FindSurfaceResidues Find buried waters Findseq Flatten obj GetNamesInSel Get Coordinates I Get Coordinates II Get raw distances Grepsel ListSelection2 List Colors List Secondary Structures List Selection Pairwise distances Removealt Rotkit SaveGroup SelInside SelectClipped Selection Exists ShowLigandWaters Split Movement Split Object Along Axis Split selection ToGroup Zero residues	Axes BbPlane BiologicalUnit BiologicalUnit/Quat Bounding Box CGO Text Cart to frac Center of mass CgoCircle Cgo arrow Cgo grid Contact Surface Cubes Distancetoatom DrawBoundingBox Draw Protein Dimensions Dump2CGO Ellipsoid Mark center Modevectors Perp maker Plane Wizard Radius of gyration RotationAxis Slerpy SuperSym Supercell Symmetry Axis TransformSelectionByCameraView
User Interface	Biochemical Scripts	System Scripts
Aa codes Apropos Distancetoatom Dynamic mesh Frame slider Get colors Grepset ImmersiveViz Inertia tensor Key Wait Make Figures Mouse modes Movie color fade Movie fade Movit ObjectByArrows ObjectFocus PDB Web Services Script PowerMate Dial OS X Pytms Quickdisplays RUCAP UM-5 Save2traj Save settings Set toggle Spectrumbar Stereo Figures Stereo ray VisLoad	AAindex Average b Color h CreateAtom Cyspka DistancesRH Distancetoatom FindSurfaceResidues Forster distance calculator ListSelection2 Load new B-factors Pairwise distances Polarpairs Propka Pucker Pytms Quickdisplays Resicolor ShowLigandWaters Show aromatics Show charged Show contacts Show hydrophilic Show hydrophobics	FetchLocal FilterByMol Find symbol LoadDir Monitor file continuously Pdbsurvey Pml2py Process All Files In Directory PythonTerminal Read PDB-String Tiff2ccp4 XML-RPC server
Third Party
Ccp4 contact Ccp4 ncont Ccp4 pisa PoseView PovRay Pymol2glmol RUCAP UM-5 Rasmolify Save Mopac Tiff2ccp4 Transform odb Wfmesh