Re: [Chimera-users] Chimera and secondary structure annotations

29 Oct 2005

      Hi Julio,
The secondary structure calculation requires all peptide backbone atoms.
In the Chimera docs it notes:
"Ksdssp uses the coordinates of the backbone atoms (N, CA, C,
     O, and optionally H) of a protein to determine which residues
     are in alpha helices and beta strands."
There is no way in Chimera to determine secondary structure from just
CA positions.
The error message you sent for pdb2mrc is a bug in the AIRS package
which is developed and maintained by Matt Baker (mbaker@bcm.tmc.edu)
at Baylor College of Medicine, not our group.  It is a problem in file
C:\Programme\EMAN\chimeraext\Airs\airsIO.py
It occurs because you have a model open in Chimera which is neither
a density map surface nor a PDB model (maybe a molecular surface or
a solid volume rendering?).  The airsIO.py code does not handle that
correctly.  You could try running it with only the PDB model open in
Chimera to avoid this problem.  Alternatively you could edit the airsIO.py
file with a text editor changing near line 32 from:
if str(model.__class__)=="VolumeViewer.surface.Surface_Model":
    			path=str(volume_data_set(model).data.path)
    		elif str(model.__class__)=="chimera.Molecule":
    			modelfile=model.openedAs
    			path=str(modelfile[0])
    		if filecheck.strip()==path:
    			path=os.path.abspath(model.name)
to
if str(model.__class__)=="VolumeViewer.surface.Surface_Model":
    			path=str(volume_data_set(model).data.path)
    		elif str(model.__class__)=="chimera.Molecule":
    			modelfile=model.openedAs
    			path=str(modelfile[0])
                        else:
                                path = ""
    		if filecheck.strip()==path:
    			path=os.path.abspath(model.name)
Just two lines are added the "else:" and the "path = ""'.  Make sure to use
this indentation if you make the change since that is important in Python
code.
I'll send the error message to Matt Baker.
Tom
...
Date: Sat, 29 Oct 2005 01:58:48 +0200
From: "Dr .Julio Ortiz" ortiz@biochem.mpg.de
To: Thomas Goddard goddard@cgl.ucsf.edu
Cc: meng@cgl.ucsf.edu
Subject: Re: Chimera and secondary structure annotations
Dear Thomas and Elaine:
Thank you very much for your answers, I checked the ksdssp command and it works
for some pdbs, but not for those that I mentioned with the ribosomes. I think
that the problem is that some pdbs from ribosomes (like 1GIX and 1GIY) do not
have complete residues (just CAs). In the case of your images, you have use
1PNS and 1PNU, and only those proteins in the 30S are complete.
I guess I need to contact some of the authors of the structures to see if the
complete coordinates are available.
Another question: I installed the new version of Chimera and when using pdb2mrc
I received an error message:

Traceback (most recent call last):
  File "C:\Programme\Chimera\share__main__.py", line 59, in ?
    value = chimeraInit.init(sys.argv)
  File "C:\Programme\Chimera\share\chimeraInit.py", line 308, in init
    tkgui.eventLoop()
  File "C:\Programme\Chimera\share\chimera\tkgui.py", line 2725, in eventLoop
    app.mainloop()
  File "C:\Programme\Chimera\bin\Lib\lib-tk\Tkinter.py", line 965, in mainloop
    self.tk.mainloop(n)
  File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py",
line 1751, in __call__
    _reporterror(self.func, args)
  File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py",
line 1814, in _reporterror
    displayerror(msg)
  File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py",
line 1377, in displayerror
    _errorReportFile.write(text + '\n')
  File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py",
line 1747, in __call__
    return apply(self.func, args)
  File "C:\Programme\Chimera\share\chimera\baseDialog.py", line 229, in <lambda>
    self.__buttonFuncName(txt))()
  File "C:\Programme\EMAN\chimeraext\Airs\pdb2mrc.py", line 73, in Apply
    targetPath=airsIO.getPath(target)
  File "C:\Programme\EMAN\chimeraext\Airs\airsIO.py", line 32, in getPath
    if filecheck.strip()==path:
UnboundLocalError: local variable 'path' referenced before assignment

I have already added the path of the EMAN in the tool menu. Could you tell me
what I am missing?
Thanks you very much,
Julio

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Thomas Goddard

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