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