Hi Bernard, Unfortunately Chimera versions 1.2304 (Oct 2006), 1.2309 (Nov 2006), and 1.2318 (Dec 2006) were all broken -- not able to save a PDB model relative to a density map, which made it hard to save fits of atomic models into maps. This was fixed on Dec 27, 2006 but there has not been a Chimera snapshot since then. You can replace a file in your Chimera distribution chimera/share/ModelPanel/writePDBdialog.py with the one attached to this email to fix the problem in 1.2304 or newer versions. The bug report for this problem is http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=3390&database=chimer... We plan on having a new Chimera snapshot this month that will include the fix. Tom # --- UCSF Chimera Copyright --- # Copyright (c) 2000 Regents of the University of California. # All rights reserved. This software provided pursuant to a # license agreement containing restrictions on its disclosure, # duplication and use. This notice must be embedded in or # attached to all copies, including partial copies, of the # software or any revisions or derivations thereof. # --- UCSF Chimera Copyright --- # # $Id: writePDBdialog.py,v 1.24 2006/12/27 22:05:52 pett Exp $ """dialog for writing models as PDB files""" from OpenSave import SaveModeless from chimera import replyobj, preferences, triggers, openModels, Molecule class WritePDBdialog(SaveModeless): keepShown = SaveModeless.default help = "UsersGuide/savemodel.html" name = "write PDB" def __init__(self): self.prefs = preferences.addCategory("write PDB dialog", preferences.HiddenCategory, optDict={"multiSavePDB": "multiple"}) self.haveTraj = False SaveModeless.__init__(self, clientPos='s', clientSticky='ewns', filters=[("PDB", "*.pdb", ".pdb")]) openModels.addAddHandler(self._modelsChange, None), openModels.addRemoveHandler(self._modelsChange, None) self._modelsChange() def configure(self, models=None, refreshList=True, selOnly=None): if models is not None: if len(models) > 1: name = "Multiple Models " elif models: name = models[0].name + " " else: name = "" self._toplevel.title("Save %sas PDB File" % name) if refreshList: self.modelList.setvalue(models) self._trajCheck() if len(models) > 1: self.multiSaveMenu.grid(row=self._msmRow, column=0, sticky='w') else: self.multiSaveMenu.grid_forget() if selOnly is not None: self.selOnlyVar.set(selOnly) def fillInUI(self, parent): SaveModeless.fillInUI(self, parent) row = 0 from chimera.widgets import MoleculeScrolledListBox, \ ModelOptionMenu self.modelList = MoleculeScrolledListBox(self.clientArea, labelpos='w', label_text="Save models:", listbox_selectmode='extended', selectioncommand=lambda: self.configure( self.modelList.getvalue(), refreshList=False)) self.modelList.grid(row=row, column=0, sticky='nsew') self.clientArea.rowconfigure(row, weight=1) self.clientArea.columnconfigure(0, weight=1) row += 1 import Tkinter, Pmw self.dispOnlyVar = Tkinter.IntVar(parent) self.dispOnlyVar.set(False) Tkinter.Checkbutton(self.clientArea, variable=self.dispOnlyVar, text="Save displayed atoms only").grid(row=row, column=0, sticky='w') row += 1 self.selOnlyVar = Tkinter.IntVar(parent) self.selOnlyVar.set(False) Tkinter.Checkbutton(self.clientArea, variable=self.selOnlyVar, text="Save selected atoms only").grid(row=row, column=0, sticky='w') row += 1 self.saveRelativeVar = Tkinter.IntVar(parent) self.saveRelativeVar.set(False) self.relativeFrame = f = Tkinter.Frame(self.clientArea) Tkinter.Checkbutton(f, variable=self.saveRelativeVar, text="Save relative to model:" ).grid(row=0, column=0, sticky='e') self.relModelMenu = ModelOptionMenu(f) self.relModelMenu.grid(row=0, column=1, sticky='w') self.saveUntransformedVar = Tkinter.IntVar(parent) self.saveUntransformedVar.set(True) self.untransformedButton = Tkinter.Checkbutton(self.clientArea, variable=self.saveUntransformedVar, text="Use untransformed coordinates") self._rfRow = row row += 1 self.frameSave = Pmw.OptionMenu(self.clientArea, labelpos='w', label_text="Save", initialitem="current frame", items=["current frame", "all frames"]) # not always shown; remember row number self._fsRow = row row += 1 from chimera import dialogs self.labelMap = { "single": "a single file", "multiple": "multiple files [appending model number]" } preferred = self.labelMap[self.prefs["multiSavePDB"]] self.multiSaveMenu = Pmw.OptionMenu(self.clientArea, labelpos='w', label_text="Save multiple models in", initialitem=preferred, items=self.labelMap.values()) # not always shown; remember row number self._msmRow = row row += 1 def map(self, *args): self.handler = triggers.addHandler("CoordSet", self._trajCheck, None) self._trajCheck() def unmap(self, *args): triggers.deleteHandler("CoordSet", self.handler) self.handler = None def Apply(self): from chimera import dialogs selOnly = self.selOnlyVar.get() paths = self.getPaths() if not paths: replyobj.error('No save location chosen.\n') return path = paths[0] models = self.modelList.getvalue() if not models: replyobj.error("No models chosen to save.\n") return if len(openModels.listIds()) > 1: if self.saveRelativeVar.get(): relModel = self.relModelMenu.getvalue() else: relModel = None else: if self.saveUntransformedVar.get(): relModel = models[0] else: relModel = None if self.haveTraj and self.frameSave.getvalue() == "all frames": allFrames=True else: allFrames=False import Midas if len(models) < 2: replyobj.status("Writing %s to %s\n" % (models[0].name, path)) Midas.write(models, relModel, path, allFrames=allFrames, dispOnly=self.dispOnlyVar.get(), selOnly=selOnly) replyobj.status("Wrote %s to %s\n" % (models[0].name, path)) return saveOpt = self.multiSaveMenu.getvalue() for key, value in self.labelMap.items(): if saveOpt == value: break self.prefs["multiSavePDB"] = key # write multiple models to multiple files if key == "multiple": if path.endswith(".pdb"): start, end = path[:-4], ".pdb" else: start, end = path, "" for m in models: modelPath = start + m.oslIdent()[1:] + end replyobj.status("Writing %s (%s) to %s\n" % (m.name, m.oslIdent(), modelPath)) Midas.write(m, relModel, modelPath, allFrames=allFrames, dispOnly=self.dispOnlyVar.get(), selOnly=selOnly) replyobj.status("Wrote %s (%s) to %s\n" % (m.name, m.oslIdent(), modelPath)) return # write multiple models to single file replyobj.status("Writing multiple models to %s\n" % path) Midas.write(models, relModel, path, allFrames=allFrames, dispOnly=self.dispOnlyVar.get(), selOnly=selOnly) replyobj.status("Wrote multiple models to %s\n" % path) def _modelsChange(self, *args): # can't query listbox, since it hangs off of same trigger if len(openModels.listIds()) > 1: self.untransformedButton.grid_forget() self.relativeFrame.grid(row=self._rfRow, column=0, sticky='w') else: self.relativeFrame.grid_forget() self.untransformedButton.grid(row=self._rfRow, column=0, sticky='w') def _trajCheck(self, *args): haveTraj = False for m in self.modelList.getvalue(): if len(m.coordSets) > 1: haveTraj = True break if haveTraj == self.haveTraj: return self.haveTraj = haveTraj if self.haveTraj: self.frameSave.grid(row=self._fsRow, column=0, sticky='w') else: self.frameSave.grid_forget() from chimera import dialogs dialogs.register(WritePDBdialog.name, WritePDBdialog)