Problem building 3D structure from smile text ...
Hi all I'm trying to build a 3D structure from this smile text: N[C@@H](C)C(=O)O But the program stops and doesn't respond to any key. The log window shows the next message: <type 'exceptions.KeyboardInterrupt'> Exception in Tk callback Function: <bound method BuildStructureDialog._placeAtoms of <BuildStructure.gui.BuildStructureDialog instance at 0x31ca3b0>> (type: <type 'instancemethod'>) Args: () Traceback (innermost last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ None File "CHIMERA/share/BuildStructure/gui.py", line 632, in _placeAtoms None File "CHIMERA/share/BuildStructure/Smiles.py", line 15, in openSmiles None File "CHIMERA/share/BuildStructure/Smiles.py", line 21, in smiles2mol None File "CHIMERA/share/BuildStructure/SOAPpy/WSDL.py", line 61, in __init__ None File "CHIMERA/lib/python2.5/urllib.py", line 82, in urlopen return opener.open(url) File "CHIMERA/lib/python2.5/urllib.py", line 190, in open return getattr(self, name)(url) File "CHIMERA/lib/python2.5/urllib.py", line 325, in open_http h.endheaders() File "CHIMERA/lib/python2.5/httplib.py", line 860, in endheaders self._send_output() File "CHIMERA/lib/python2.5/httplib.py", line 732, in _send_output self.send(msg) File "CHIMERA/lib/python2.5/httplib.py", line 699, in send self.connect() File "CHIMERA/lib/python2.5/httplib.py", line 673, in connect self.sock.connect(sa) File "<string>", line 1, in connect None <type 'exceptions.KeyboardInterrupt'>: Am I doing something wrong? I am working with this chimera version: alpha version, build 2577, 2008/12/09 -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221
Hi Sergio, Normally if you want to report an error it is best to use "Help... Report a Bug" in the Chimera menu since that would automatically include information about your computer and Chimera version, and let you attach files. However, in this case I can immediately see the problem: you need a newer version of Chimera! You would need a version from July 3 or later, for example the August 20 snapshot: <http://www.cgl.ucsf.edu/chimera/download.html#snapshots> Explanation: The SMILES -> 3D structure conversion is done by a Web server provided by a group at Indiana University, and a few months ago they changed how this service is accessed. It was necessary to change Chimera to use the new, updated service. I tested the following command in the snapshot version just now, and it worked fine: open smiles:N[C@@H](C)C(=O)O Using this command is the same as entering the SMILES in the Build Structure dialog. I also checked doing it that way. I think you will be pleasantly surprised to see the many improvements we have made in Build Structure and in other tools, and the many new features that have been added to Chimera! Improvements between 1.3 and the snapshot (and you were using a version older than 1.3): <http://www.cgl.ucsf.edu/chimera/1.4_b28596/docs/relnotes/snapshot.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
participants (2)
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Elaine Meng -
Sergio Garay