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 Post subject: data player help
PostPosted: Sat Aug 31, 2013 3:13 pm 
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Millimolar User
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Joined: Mon Jul 29, 2013 12:10 am
Posts: 8
I'm working on trying to get the data player to work. I'm following the first advanced ePMV tutorial for c4d and so far I have a model of emd_1097.ccp4 rendered in my viewport, but in the Apply dropdown the selection is set to None, and there are no more options, so it looks like I can't select my emd import? Please let me know if I missed a step. Thanks


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 Post subject: Re: data player help
PostPosted: Sun Sep 01, 2013 12:10 am 
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Joined: Wed Apr 22, 2009 2:08 am
Posts: 235
Hi,
Sometimes it help if you first load a molecule, but it shouldn't.
Could you do it again and send me the content of the console to see the error message, as it should show you:
-None
-emd_1097.ccp4
in the drop down menu next to Apply

Ludo


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 Post subject: Re: data player help
PostPosted: Sat Sep 14, 2013 4:25 pm 
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Joined: Mon Jul 29, 2013 12:10 am
Posts: 8
Sorry for the late response. Here is my console output
Code:
(0, 'mp_556298', ['mp_556298', 'mp_24733', 'znp2_11025', 'znp2_11025_3', 'znp2_11025_4', 'NaP2H5O8_505701', 'br_23154', 'Mn_542909', 'Mn_542909'])
CCP4 file: /Plugins/ePMV-Mac/emd_1097.ccp4
mode: 2
indices (1:fastest, 3:slowest) 1 2 3
nc: 128, nr: 128, ns: 128
dimensions: (128, 128, 128)
origin: 0.0, 0.0, 0.0
acell: 2099.199951, bcell: 2099.199951, ccell: 2099.199951
alpha:  90.000000, beta:  90.000000, gamma:  90.000000
symmetry ops: 0 bytes in length
Skew transformation Flag = 0
min:   -5.666581
max:     6.686424
mean:   0.000000
stdev:   1.000000
time to read file:  2.19245791435
doit addGriddoit addGriddoit addGridDone('isoC', 'grid_1IsoSurface')
{'mini': -10.0, 'sub': None, 'name': 'state', 'show': True, 'trigger': False, 'precision': 4.0, 'value': None, 'height': 10, 'width': 100, 'step': 0.01, 'maxi': 10.0, 'variable': 0.0, 'tooltip': '', 'action': <bound method epmvGui.applyState of <ePMV.epmvGui.epmvGui object at 0x118e446e0>>, 'label': 'step/value', 'type': 'sliders', 'id': 1102, 'alignement': 59, 'icon': None} 0.0
<type 'float'>
('nData', 1)
menu 1052
menu 1123
(0, 'mp_556298', ['mp_556298', 'mp_24733', 'znp2_11025', 'znp2_11025_3', 'znp2_11025_4', 'NaP2H5O8_505701', 'br_23154', 'Mn_542909', 'Mn_542909'])
CCP4 file: /Plugins/ePMV-Mac/emd_1097.ccp4
mode: 2
indices (1:fastest, 3:slowest) 1 2 3
nc: 128, nr: 128, ns: 128
dimensions: (128, 128, 128)
origin: 0.0, 0.0, 0.0
acell: 2099.199951, bcell: 2099.199951, ccell: 2099.199951
alpha:  90.000000, beta:  90.000000, gamma:  90.000000
symmetry ops: 0 bytes in length
Skew transformation Flag = 0
min:   -5.666581
max:     6.686424
mean:   0.000000
stdev:   1.000000
time to read file:  2.07287311554
doit addGriddoit addGriddoit addGridDone('isoC', 'grid_2IsoSurface')
{'mini': -10.0, 'sub': None, 'name': 'state', 'show': True, 'trigger': False, 'precision': 4.0, 'value': None, 'height': 10, 'width': 100, 'step': 0.01, 'maxi': 10.0, 'variable': 0.0, 'tooltip': '', 'action': <bound method epmvGui.applyState of <ePMV.epmvGui.epmvGui object at 0x118e446e0>>, 'label': 'step/value', 'type': 'sliders', 'id': 1102, 'alignement': 59, 'icon': None} 0.0
<type 'float'>
('nData', 1)
Traceback (most recent call last):
  File "/Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/ePMV/epmvGui.py", line 1389, in Command
    self._command(args)
  File "/Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/upy/uiAdaptor.py", line 155, in _command
    self._callElem(line,evt)
  File "/Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/upy/uiAdaptor.py", line 122, in _callElem
    self._callElemAction(elem)
  File "/Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/upy/uiAdaptor.py", line 106, in _callElemAction
    self.callbackaction(item)
  File "/Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/upy/uiAdaptor.py", line 79, in callbackaction
    item['action'](*args)
  File "/Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/ePMV/epmvGui.py", line 2207, in browseDATA
    self.fileDialog(label="choose a data file",callback=self.loadDATA)
  File "/Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/upy/cinema4d/r14/c4dUI.py", line 645, in fileDialog
    return callback(filename)
  File "/Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/ePMV/epmvGui.py", line 2191, in loadDATA
    else : self.gridData(file=filename,dataname=dataname+extension)
  File "/Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/ePMV/epmvGui.py", line 2340, in gridData
    self.addItemToPMenu(self.COMB_BOX["dat"],os.path.basename(trajname))
  File "/Applications/MAXON/CINEMA 4D R14/resource/modules/python/res/Python.osx.framework/lib/python2.6/posixpath.py", line 111, in basename
    i = p.rfind('/') + 1
AttributeError: 'NoneType' object has no attribute 'rfind'
menu 1055


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 Post subject: Re: data player help
PostPosted: Sat Sep 14, 2013 5:32 pm 
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Joined: Mon Jul 29, 2013 12:10 am
Posts: 8
Another problem I found is with using the modeller. I followed the modeller extension tutorial with the example 1TIMtr.pdb file and it worked fine...but whenever I tried to import a diff .pdb file with the same ePMV preferences checked, i got an import error (even though i could successfully import the same pdb files with the 'user modeller' preference unchecked). Is there something unique about that example pdb file that makes it work with the modeller?

here is the console output if it helps:

Code:

Traceback (most recent call last):
  File "Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/ePMV/epmvGui.py", line 1389, in Command
    self._command(args)
  File "Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/upy/uiAdaptor.py", line 155, in _command
    self._callElem(line,evt)
  File "Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/upy/uiAdaptor.py", line 122, in _callElem
    self._callElemAction(elem)
  File "Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/upy/uiAdaptor.py", line 106, in _callElemAction
    self.callbackaction(item)
  File "Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/upy/uiAdaptor.py", line 79, in callbackaction
    item['action'](*args)
  File "Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/ePMV/epmvGui.py", line 2691, in delete_Atom_Selection
    if sel is mol.name :
AttributeError: 'NoneType' object has no attribute 'name'
Traceback (most recent call last):
  File "Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/ePMV/epmvGui.py", line 1389, in Command
    self._command(args)
  File "Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/upy/uiAdaptor.py", line 155, in _command
    self._callElem(line,evt)
  File "Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/upy/uiAdaptor.py", line 122, in _callElem
    self._callElemAction(elem)
  File "Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/upy/uiAdaptor.py", line 106, in _callElemAction
    self.callbackaction(item)
  File "Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/upy/uiAdaptor.py", line 79, in callbackaction
    item['action'](*args)
  File "Library/Preferences/MAXON/CINEMA 4D R14_95696CEA/plugins/ePMV/mgl64//MGLToolsPckgs/ePMV/epmvGui.py", line 2691, in delete_Atom_Selection
    if sel is mol.name :
AttributeError: 'NoneType' object has no attribute 'name'
menu 1012
(<ePMV.epmvGui.Parameter_epmvGUI object at 0x11cfd52d0>, 2555554, True)
('center_mol', {'mini': 0, 'sub': None, 'name': 'Center molecule to origin', 'show': True, 'trigger': False, 'precision': 4.0, 'value': True, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': True, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1007, 'alignement': 59, 'icon': None}, True)
('use_instances', {'mini': 0, 'sub': None, 'name': 'Build instances for atoms and bonds', 'show': True, 'trigger': False, 'precision': 4.0, 'value': True, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': True, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1016, 'alignement': 59, 'icon': None}, True)
('removeWater', {'mini': 0, 'sub': None, 'name': 'Remove water', 'show': True, 'trigger': False, 'precision': 4.0, 'value': True, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': True, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1022, 'alignement': 59, 'icon': None}, True)
('synchro_realtime', {'mini': 0, 'sub': None, 'name': 'Viewport changes modify PDB data (Synchro realtime)', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1017, 'alignement': 59, 'icon': None}, False)
('updateColor', {'mini': 0, 'sub': None, 'name': 'Update color automatically for multi-state models', 'show': True, 'trigger': False, 'precision': 4.0, 'value': True, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': True, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1008, 'alignement': 59, 'icon': None}, True)
('uniq_ss', {'mini': 0, 'sub': None, 'name': 'Single colorizable mesh for Ribbon and Beaded Ribbon', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1009, 'alignement': 59, 'icon': None}, False)
('build_bonds', {'mini': 0, 'sub': None, 'name': 'Build bonds by distance, with', 'show': True, 'trigger': False, 'precision': 4.0, 'value': True, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': True, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1010, 'alignement': 59, 'icon': None}, True)
('doCamera', {'mini': 0, 'sub': None, 'name': 'PMV camera', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1020, 'alignement': 59, 'icon': None}, False)
('use_progressBar', {'mini': 0, 'sub': None, 'name': 'Progress bar', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1023, 'alignement': 59, 'icon': None}, False)
('bicyl', {'mini': 0, 'sub': None, 'name': 'Split bonds (slower)', 'show': True, 'trigger': False, 'precision': 4.0, 'value': True, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': True, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1005, 'alignement': 59, 'icon': None}, True)
('forceFetch', {'mini': 0, 'sub': None, 'name': 'Override cache version when [Fetch]ing new molecule', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1021, 'alignement': 59, 'icon': None}, False)
('doLight', {'mini': 0, 'sub': None, 'name': 'PMV light', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1011, 'alignement': 59, 'icon': None}, False)
('ribcolor', {'mini': 0, 'sub': None, 'name': 'use vertex color for ribbon geometry', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1012, 'alignement': 59, 'icon': None}, False)
('useModeller', {'mini': 0, 'sub': None, 'name': 'Use Modeller', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1025, 'alignement': 59, 'icon': None}, False)
('force_pross', {'mini': 0, 'sub': None, 'name': 'Force PROSS (override pdb file SS)', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1026, 'alignement': 59, 'icon': None}, False)
('usePymol', {'mini': 0, 'sub': None, 'name': 'Use PyMOL', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1013, 'alignement': 59, 'icon': None}, False)
('bonds_threshold', {'mini': 0.0, 'sub': None, 'name': 'bonds distance cutoff', 'show': True, 'trigger': False, 'precision': 4.0, 'value': 1.1000000000000001, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10.0, 'variable': 1.1000000000000001, 'tooltip': '', 'action': None, 'label': None, 'type': 'inputFloat', 'id': 1015, 'alignement': 59, 'icon': None}, 1.1000000000000001)
{'mini': 0.0, 'sub': None, 'name': 'bonds distance cutoff', 'show': True, 'trigger': False, 'precision': 4.0, 'value': 1.1000000000000001, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10.0, 'variable': 1.1000000000000001, 'tooltip': '', 'action': None, 'label': None, 'type': 'inputFloat', 'id': 1015, 'alignement': 59, 'icon': None} 1.1
<type 'float'>
('join_ss', {'mini': 0, 'sub': None, 'name': 'Connect Ribbon geometry', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1006, 'alignement': 59, 'icon': None}, False)
('center_grid', {'mini': 0, 'sub': None, 'name': 'Center Grid', 'show': True, 'trigger': False, 'precision': 4.0, 'value': True, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': True, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1024, 'alignement': 59, 'icon': None}, True)
('center_mol', {'mini': 0, 'sub': None, 'name': 'Center molecule to origin', 'show': True, 'trigger': False, 'precision': 4.0, 'value': True, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': True, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1007, 'alignement': 59, 'icon': None}, True)
('use_instances', {'mini': 0, 'sub': None, 'name': 'Build instances for atoms and bonds', 'show': True, 'trigger': False, 'precision': 4.0, 'value': True, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': True, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1016, 'alignement': 59, 'icon': None}, True)
('removeWater', {'mini': 0, 'sub': None, 'name': 'Remove water', 'show': True, 'trigger': False, 'precision': 4.0, 'value': True, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': True, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1022, 'alignement': 59, 'icon': None}, True)
('synchro_realtime', {'mini': 0, 'sub': None, 'name': 'Viewport changes modify PDB data (Synchro realtime)', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1017, 'alignement': 59, 'icon': None}, False)
('updateColor', {'mini': 0, 'sub': None, 'name': 'Update color automatically for multi-state models', 'show': True, 'trigger': False, 'precision': 4.0, 'value': True, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': True, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1008, 'alignement': 59, 'icon': None}, True)
('uniq_ss', {'mini': 0, 'sub': None, 'name': 'Single colorizable mesh for Ribbon and Beaded Ribbon', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1009, 'alignement': 59, 'icon': None}, False)
('build_bonds', {'mini': 0, 'sub': None, 'name': 'Build bonds by distance, with', 'show': True, 'trigger': False, 'precision': 4.0, 'value': True, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': True, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1010, 'alignement': 59, 'icon': None}, True)
('doCamera', {'mini': 0, 'sub': None, 'name': 'PMV camera', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1020, 'alignement': 59, 'icon': None}, False)
('use_progressBar', {'mini': 0, 'sub': None, 'name': 'Progress bar', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1023, 'alignement': 59, 'icon': None}, False)
('bicyl', {'mini': 0, 'sub': None, 'name': 'Split bonds (slower)', 'show': True, 'trigger': False, 'precision': 4.0, 'value': True, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': True, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1005, 'alignement': 59, 'icon': None}, True)
('forceFetch', {'mini': 0, 'sub': None, 'name': 'Override cache version when [Fetch]ing new molecule', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1021, 'alignement': 59, 'icon': None}, False)
('doLight', {'mini': 0, 'sub': None, 'name': 'PMV light', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1011, 'alignement': 59, 'icon': None}, False)
('ribcolor', {'mini': 0, 'sub': None, 'name': 'use vertex color for ribbon geometry', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1012, 'alignement': 59, 'icon': None}, False)
('useModeller', {'mini': 0, 'sub': None, 'name': 'Use Modeller', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1025, 'alignement': 59, 'icon': None}, False)
('force_pross', {'mini': 0, 'sub': None, 'name': 'Force PROSS (override pdb file SS)', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1026, 'alignement': 59, 'icon': None}, False)
('usePymol', {'mini': 0, 'sub': None, 'name': 'Use PyMOL', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1013, 'alignement': 59, 'icon': None}, False)
('bonds_threshold', {'mini': 0.0, 'sub': None, 'name': 'bonds distance cutoff', 'show': True, 'trigger': False, 'precision': 4.0, 'value': 1.1000000000000001, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10.0, 'variable': 1.1000000000000001, 'tooltip': '', 'action': None, 'label': None, 'type': 'inputFloat', 'id': 1015, 'alignement': 59, 'icon': None}, 1.1000000000000001)
{'mini': 0.0, 'sub': None, 'name': 'bonds distance cutoff', 'show': True, 'trigger': False, 'precision': 4.0, 'value': 1.1000000000000001, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10.0, 'variable': 1.1000000000000001, 'tooltip': '', 'action': None, 'label': None, 'type': 'inputFloat', 'id': 1015, 'alignement': 59, 'icon': None} 1.1
<type 'float'>
('join_ss', {'mini': 0, 'sub': None, 'name': 'Connect Ribbon geometry', 'show': True, 'trigger': False, 'precision': 4.0, 'value': False, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': False, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1006, 'alignement': 59, 'icon': None}, False)
('center_grid', {'mini': 0, 'sub': None, 'name': 'Center Grid', 'show': True, 'trigger': False, 'precision': 4.0, 'value': True, 'height': 10, 'width': 180, 'step': 1, 'maxi': 10, 'variable': True, 'tooltip': '', 'action': None, 'label': None, 'type': 'checkbox', 'id': 1024, 'alignement': 59, 'icon': None}, True)
                         MODELLER 9.12, 2013/06/12, r9480
     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
                     Copyright(c) 1989-2013 Andrej Sali
                            All Rights Reserved
                             Written by A. Sali
                               with help from
           B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,
                N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser,
                    R. Sanchez, B. Yerkovich, A. Badretdinov,
                      F. Melo, J.P. Overington, E. Feyfant
                 University of California, San Francisco, USA
                    Rockefeller University, New York, USA
                      Harvard University, Cambridge, USA
                   Imperial Cancer Research Fund, London, UK
              Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Darwin Miriam-2.local 12.4.0 x86_64
Date and time of compilation         : 2013/06/11 21:19:51
MODELLER executable type             : mac10v4-intel64
Job starting time (YY/MM/DD HH:MM:SS): 2013/09/14 10:25:10
read_to_681_> topology.submodel read from topology file:        3
__init__
init
Traceback (most recent call last):
  File "'epmv_synchro.pyp'", line 52, in Execute
AttributeError: Protein instance has no attribute 'name'
Traceback (most recent call last):
  File "'epmv_synchro.pyp'", line 52, in Execute
AttributeError: Protein instance has no attribute 'name'
rdpdb___303E> No atoms were read from the specified input PDB file, since the
              starting residue number and/or chain id in MODEL_SEGMENT (or
              the alignment file header) was not found;
              requested starting position: residue number " FIRST", chain " @";
              atom file name:  /periodic table/li-567337.pdb
menu 1053
Traceback (most recent call last):
  File "'epmv_synchro.pyp'", line 52, in Execute
AttributeError: Protein instance has no attribute 'name'
Traceback (most recent call last):
  File "'epmv_synchro.pyp'", line 52, in Execute
AttributeError: Protein instance has no attribute 'name'



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 Post subject: Re: data player help
PostPosted: Sun Oct 06, 2013 2:35 am 
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Joined: Wed Nov 10, 2010 1:19 am
Posts: 19
Hi Volvox,
Sorry for the slow reply- we've been working hard on other stuff lately. It appears to me that you are trying to load some custom pdb file "li-567337.pdb". When you load that file with standard ePMV, it uses a library built into the underlying software PMV called molkit to read the file and generate the structure. When you select [√] Use modeller, the 3rd party Modeller software overrrides PMV to read the pdb file and rebuild it into a modeller friendly format. It appears that Modeller didn't like your file for some reason– many PDB readers/parsers are very particular about formatting, especially in regards to endOfLine character types, etc. So if you're using a custom PDB, make sure it follows all of the rules.

You can try to open it in ePMV, then save the molecule as a PDB file, then open that file with modeller to see if PMV fixes any of the issues in the original file. Also try exporting the PDB from Chimera or Pymol for example.

Lastly, I'm not sure what other restrictions there are on the default modeller import, but if you want to post your file here or to info@autopack.org, we can take a look and try to get it running or debug.

Please let us know if it works, and again, sorry for the delayed reply.
Graham


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