MultiFit is not working
Dear Chimera-team, I was trying to use a MultiFit service of Chimera (to fit two models into my cryo density map), and it gives me the following error: Wrote /tmp/tmp_rSyaW/INSRT_model2.pdb Wrote /tmp/tmp_rSyaW/1x1n.pdb Traceback from web service request (connection setup): Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 52, in _setup md = self.sudsClient.service.getAppMetadata() File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 280, in __getattr__ port = self.__find(0) File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 315, in __find raise Exception, 'No services defined' Exception: No services defined Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from web application request: Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:MultiFitWebService' is unavailable. See Reply Log for more details. Could you please give me a clue what might be a problem. I do have an internet connection (checked by 'Fletch by ID... ' function) Thank you for your support, Julia
Hi Julia, I can only suggest reading the error message from Chimera (which you included below) and following its suggestions. See below, starting “Typically…” Basically it says the web service is down but should be up later. I tried the MultiFit web service and it is running now, so maybe it would work if you just tried again. Alternatively, instead of MultiFit, you could try the “fitmap” command, which can fit multiple structures sequentially or do symmetric fitting without using a web service. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 2, 2016, at 5:23 AM, Smirnova, Julia <julia.smirnova@charite.de> wrote:
Dear Chimera-team,
I was trying to use a MultiFit service of Chimera (to fit two models into my cryo density map), and it gives me the following error:
Wrote /tmp/tmp_rSyaW/INSRT_model2.pdb Wrote /tmp/tmp_rSyaW/1x1n.pdb Traceback from web service request (connection setup): Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 52, in _setup md = self.sudsClient.service.getAppMetadata() File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 280, in __getattr__ port = self.__find(0) File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 315, in __find raise Exception, 'No services defined' Exception: No services defined
Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from web application request: Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:MultiFitWebService' is unavailable. See Reply Log for more details.
Could you please give me a clue what might be a problem.
I do have an internet connection (checked by 'Fletch by ID... ' function)
Thank you for your support, Julia
Dear Elaine, thank you for reply! Somehow it still does not work. I will try also a fitmap function, I have several pdb models to fit into my cryo em map. And I was thinking that multiFit could help me with that better. Best, julia ________________________________________ Von: Elaine Meng [meng@cgl.ucsf.edu] Gesendet: Mittwoch, 2. November 2016 19:38 An: Smirnova, Julia Cc: chimera-users@cgl.ucsf.edu Betreff: Re: [Chimera-users] MultiFit is not working Hi Julia, I can only suggest reading the error message from Chimera (which you included below) and following its suggestions. See below, starting “Typically…” Basically it says the web service is down but should be up later. I tried the MultiFit web service and it is running now, so maybe it would work if you just tried again. Alternatively, instead of MultiFit, you could try the “fitmap” command, which can fit multiple structures sequentially or do symmetric fitting without using a web service. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 2, 2016, at 5:23 AM, Smirnova, Julia <julia.smirnova@charite.de> wrote:
Dear Chimera-team,
I was trying to use a MultiFit service of Chimera (to fit two models into my cryo density map), and it gives me the following error:
Wrote /tmp/tmp_rSyaW/INSRT_model2.pdb Wrote /tmp/tmp_rSyaW/1x1n.pdb Traceback from web service request (connection setup): Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 52, in _setup md = self.sudsClient.service.getAppMetadata() File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 280, in __getattr__ port = self.__find(0) File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 315, in __find raise Exception, 'No services defined' Exception: No services defined
Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from web application request: Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:MultiFitWebService' is unavailable. See Reply Log for more details.
Could you please give me a clue what might be a problem.
I do have an internet connection (checked by 'Fletch by ID... ' function)
Thank you for your support, Julia
Can you try again? I see MultiFit jobs running on our server as I type this, so perhaps this was some kind of temporary problem, or a connectivity problem between your site and ours. If the problem continues, please use Help->Report A Bug to make a report, which will automatically include a lot of details about the machine you are using and the version of Chimera. Thanks. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Nov 2, 2016, at 5:23 AM, Smirnova, Julia <julia.smirnova@charite.de> wrote:
Dear Chimera-team,
I was trying to use a MultiFit service of Chimera (to fit two models into my cryo density map), and it gives me the following error:
Wrote /tmp/tmp_rSyaW/INSRT_model2.pdb Wrote /tmp/tmp_rSyaW/1x1n.pdb Traceback from web service request (connection setup): Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 52, in _setup md = self.sudsClient.service.getAppMetadata() File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 280, in __getattr__ port = self.__find(0) File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 315, in __find raise Exception, 'No services defined' Exception: No services defined
Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from web application request: Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:MultiFitWebService' is unavailable. See Reply Log for more details.
Could you please give me a clue what might be a problem.
I do have an internet connection (checked by 'Fletch by ID... ' function)
Thank you for your support, Julia
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Hi Eric, thank you for reply and advises! Today it gives me the same error. And when I try to submit it to the 'Report a Bug' it gives me another error: gaierror Exception in Tk callback Function: <bound method BugReportGUI.Submit of <BugReport.BugReportGUI.BugReportGUI object at 0x7f8b9709d250>> (type: <type 'instancemethod'>) Module: <module 'BugReport.BugReportGUI' from '/opt/UCSF/Chimera64-1.11.2rc/share/BugReport/BugReportGUI.pyc'> (line: 348) Args: () Traceback (innermost last): File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/opt/UCSF/Chimera64-1.11.2rc/share/BugReport/BugReportGUI.py", line 426, in Submit BUG_SELECTOR, fields) File "/opt/UCSF/Chimera64-1.11.2rc/share/CGLutil/multipart.py", line 29, in post_multipart_formdata h.endheaders() File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/httplib.py", line 1049, in endheaders self._send_output(message_body) File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/httplib.py", line 893, in _send_output self.send(msg) File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/httplib.py", line 855, in send self.connect() File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/httplib.py", line 832, in connect self.timeout, self.source_address) File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/socket.py", line 557, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): gaierror: [Errno -2] Name or service not known gaierror: [Errno -2] Name or service not known File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/socket.py", line 557, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): See reply log for Python traceback. Our IT support guy is not aware of what could be wrong.. Thank you, Julia ________________________________ Von: Eric Pettersen [pett@cgl.ucsf.edu] Gesendet: Mittwoch, 2. November 2016 19:41 An: Smirnova, Julia Cc: chimera-users@cgl.ucsf.edu Betreff: Re: [Chimera-users] MultiFit is not working Can you try again? I see MultiFit jobs running on our server as I type this, so perhaps this was some kind of temporary problem, or a connectivity problem between your site and ours. If the problem continues, please use Help->Report A Bug to make a report, which will automatically include a lot of details about the machine you are using and the version of Chimera. Thanks. —Eric Eric Pettersen UCSF Computer Graphics Lab On Nov 2, 2016, at 5:23 AM, Smirnova, Julia <julia.smirnova@charite.de<mailto:julia.smirnova@charite.de>> wrote: Dear Chimera-team, I was trying to use a MultiFit service of Chimera (to fit two models into my cryo density map), and it gives me the following error: Wrote /tmp/tmp_rSyaW/INSRT_model2.pdb Wrote /tmp/tmp_rSyaW/1x1n.pdb Traceback from web service request (connection setup): Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 52, in _setup md = self.sudsClient.service.getAppMetadata() File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 280, in __getattr__ port = self.__find(0) File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 315, in __find raise Exception, 'No services defined' Exception: No services defined Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from web application request: Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:MultiFitWebService' is unavailable. See Reply Log for more details. Could you please give me a clue what might be a problem. I do have an internet connection (checked by 'Fletch by ID... ' function) Thank you for your support, Julia _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
This error is a networking error. For some reason, Chimera on your computer can't reach www.cgl.ucsf.edu. Googling 'gaierror: Name or service not known', I see that there are many possible causes of this problem. In one case, it happens if the first nameserver that is checked for www.cgl.ucsf.edu doesn't support recursion and reordering the nameservers in /etc/resolv.conf fixed the problem. Not being able to access www.cgl.ucsf.edu would explain your problem with MultiFit too. Please forward this information to your IT support guy. -- Greg On 11/03/2016 06:40 AM, Smirnova, Julia wrote:
Hi Eric,
thank you for reply and advises!
Today it gives me the same error. And when I try to submit it to the 'Report a Bug' it gives me another error:
gaierror Exception in Tk callback Function: <bound method BugReportGUI.Submit of <BugReport.BugReportGUI.BugReportGUI object at 0x7f8b9709d250>> (type: <type 'instancemethod'>) Module: <module 'BugReport.BugReportGUI' from '/opt/UCSF/Chimera64-1.11.2rc/share/BugReport/BugReportGUI.pyc'> (line: 348) Args: () Traceback (innermost last): File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/opt/UCSF/Chimera64-1.11.2rc/share/BugReport/BugReportGUI.py", line 426, in Submit BUG_SELECTOR, fields) File "/opt/UCSF/Chimera64-1.11.2rc/share/CGLutil/multipart.py", line 29, in post_multipart_formdata h.endheaders() File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/httplib.py", line 1049, in endheaders self._send_output(message_body) File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/httplib.py", line 893, in _send_output self.send(msg) File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/httplib.py", line 855, in send self.connect() File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/httplib.py", line 832, in connect self.timeout, self.source_address) File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/socket.py", line 557, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): gaierror: [Errno -2] Name or service not known
gaierror: [Errno -2] Name or service not known
File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/socket.py", line 557, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM):
See reply log for Python traceback.
Our IT support guy is not aware of what could be wrong..
Thank you, Julia
------------------------------------------------------------------------ *Von:* Eric Pettersen [pett@cgl.ucsf.edu] *Gesendet:* Mittwoch, 2. November 2016 19:41 *An:* Smirnova, Julia *Cc:* chimera-users@cgl.ucsf.edu *Betreff:* Re: [Chimera-users] MultiFit is not working
Can you try again? I see MultiFit jobs running on our server as I type this, so perhaps this was some kind of temporary problem, or a connectivity problem between your site and ours. If the problem continues, please use Help->Report A Bug to make a report, which will automatically include a lot of details about the machine you are using and the version of Chimera. Thanks.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 2, 2016, at 5:23 AM, Smirnova, Julia <julia.smirnova@charite.de <mailto:julia.smirnova@charite.de>> wrote:
Dear Chimera-team,
I was trying to use a MultiFit service of Chimera (to fit two models into my cryo density map), and it gives me the following error:
Wrote /tmp/tmp_rSyaW/INSRT_model2.pdb Wrote /tmp/tmp_rSyaW/1x1n.pdb Traceback from web service request (connection setup): Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 52, in _setup md = self.sudsClient.service.getAppMetadata() File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 280, in __getattr__ port = self.__find(0) File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 315, in __find raise Exception, 'No services defined' Exception: No services defined
Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from web application request: Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:MultiFitWebService' is unavailable. See Reply Log for more details.
Could you please give me a clue what might be a problem.
I do have an internet connection (checked by 'Fletch by ID... ' function)
Thank you for your support, Julia
_______________________________________________ Chimera-users mailing list:Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription:http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Elaine Meng -
Eric Pettersen -
Greg Couch -
Smirnova, Julia