Dear chimera users, I'm trying comparative modeling tutorial in chimera tutorials and I'm getting the following error in using fetch uniprot id. *Steps followed: * Menu--> fetch by ID--> selected uniprot--> "oprd_human" "P41143" (tried all combinations) *Error:* *BadStatusLine: '' File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status raise BadStatusLine(line) See reply log for Python traceback. * I tried changing the preference to use "http" but nothing fix it. please help. -- regards, Pavithra.K.B.
Dear chimera users, I'm trying comparative modeling tutorial in chimera tutorials and I'm getting the following error in using fetch uniprot id. *Steps followed: * Menu--> fetch by ID--> selected uniprot--> "oprd_human" "P41143" (tried all combinations) *Error:* *BadStatusLine: '' File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status raise BadStatusLine(line) See reply log for Python traceback. * I tried changing the preference to use "http" but nothing fix it. please help. The detailed error is given below <class 'httplib.BadStatusLine'> Exception in Tk callback Function: <bound method MidasUI.processCommand of <Midas.midas_ui.MidasUI instance at 0x048CA508>> (type: <type 'instancemethod'>) Args: (<Tkinter.Event instance at 0x064D9300>,) Event type: KeyPress (type num: 2) Traceback (innermost last): File "C:\Program Files\Chimera 1.7\bin\lib\site-packages\Pmw\Pmw_1_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.7\share\Midas\midas_ui.py", line 270, in processCommand midas_text.makeCommand(cmdText) File "C:\Program Files\Chimera 1.7\share\Midas\midas_text.py", line 69, in makeCommand f(c, args) File "C:\Program Files\Chimera 1.7\share\Midas\midas_text.py", line 1449, in doOpen modelArg, noprefs) File "<string>", line 1, in <module> None File "C:\Program Files\Chimera 1.7\share\Midas\__init__.py", line 2033, in open noprefs=noprefs) File "C:\Program Files\Chimera 1.7\share\chimera\__init__.py", line 1745, in open models = func(filename, *args, **kw) File "C:\Program Files\Chimera 1.7\share\SeqAnnotations\ChimeraExtension.py", line 27, in showUniprotSeq self.module().showUniprotSeq(ident) File "C:\Program Files\Chimera 1.7\share\SeqAnnotations\__init__.py", line 302, in showUniprotSeq acc = mapUniprotNameID(ident) File "C:\Program Files\Chimera 1.7\share\SeqAnnotations\__init__.py", line 62, in mapUniprotNameID response = urllib2.urlopen(request) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 126, in urlopen return _opener.open(url, data, timeout) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 406, in open response = meth(req, response) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 519, in http_response 'http', request, response, code, msg, hdrs) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 438, in error result = self._call_chain(*args) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 378, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 625, in http_error_302 return self.parent.open(new, timeout=req.timeout) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 400, in open response = self._open(req, data) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 418, in _open '_open', req) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 378, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 1207, in http_open return self.do_open(httplib.HTTPConnection, req) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 1180, in do_open r = h.getresponse(buffering=True) File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 1030, in getresponse response.begin() File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 407, in begin version, status, reason = self._read_status() File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status raise BadStatusLine(line) <class 'httplib.BadStatusLine'>: '' ================================================ Event contents: char: delta: 13 height: ?? keycode: 13 keysym: Return keysym_num: 65293 num: ?? serial: 38444 state: 8 time: 69416531 type: 2 widget: .44391680.76326552.76670056.76670616.76670816 width: ?? x: 174 x_root: 227 y: 13 y_root: 942 BadStatusLine: '' File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status raise BadStatusLine(line) See reply log for Python traceback. -- regards, Pavithra.K.B.
Hi Pavithra, I can't reproduce this problem -- the fetch of UniProt oprd_human is successful for me in Chimera 1.7 and newer versions of Chimera. I don't know what preference you are talking about... if you meant the download directory, that only specifies a local directory for saving the files and should not have "http" in it. In general, you should report problems using the Chimera menu: Help... Report a Bug instead of sending email to this address. In the report form, you can include a description of what you did and your email (if you want feedback). Some other things to try and maybe mention in the report: can you fetch anything from UniProt? Can you fetch anything from any database (PDB, etc.)? Thanks 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 Oct 23, 2013, at 6:01 PM, Pavithra wrote:
Dear chimera users,
I'm trying comparative modeling tutorial in chimera tutorials and I'm getting the following error in using fetch uniprot id.
Steps followed: Menu--> fetch by ID--> selected uniprot--> "oprd_human" "P41143" (tried all combinations)
Error:
BadStatusLine: ''
File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status raise BadStatusLine(line)
See reply log for Python traceback.
I tried changing the preference to use "http" but nothing fix it. please help.
-- regards, Pavithra.K.B. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Dr. Elaine, Thank you for the reply. I tried to report the bug before I mailed this group. To be exact for the past two days, I tried to report the bug. But, It didn't work. The preference I was talking about is the "web access" in which i changed the http proxy true and tried. I have tried Fetching pdb, Emdb, which was successful. But, with uniprot I'm getting the previously mentioned error. I have tried different uniprot Ids but I get the same error. On Thu, Oct 24, 2013 at 10:18 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pavithra, I can't reproduce this problem -- the fetch of UniProt oprd_human is successful for me in Chimera 1.7 and newer versions of Chimera. I don't know what preference you are talking about... if you meant the download directory, that only specifies a local directory for saving the files and should not have "http" in it.
In general, you should report problems using the Chimera menu: Help... Report a Bug instead of sending email to this address. In the report form, you can include a description of what you did and your email (if you want feedback). Some other things to try and maybe mention in the report: can you fetch anything from UniProt? Can you fetch anything from any database (PDB, etc.)? Thanks 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 Oct 23, 2013, at 6:01 PM, Pavithra wrote:
Dear chimera users,
I'm trying comparative modeling tutorial in chimera tutorials and I'm getting the following error in using fetch uniprot id.
Steps followed: Menu--> fetch by ID--> selected uniprot--> "oprd_human" "P41143" (tried all combinations)
Error:
BadStatusLine: ''
File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status raise BadStatusLine(line)
See reply log for Python traceback.
I tried changing the preference to use "http" but nothing fix it. please help.
-- regards, Pavithra.K.B. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- regards, Pavithra.K.B.
Hi Pavithra, Thanks for reporting the error via the bug-reporting mechanism. Since this problem seems to be affecting no one else, we'll work on it via the bug report rather than via the users list. Expect mail via the bug report soon. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 23, 2013, at 7:12 PM, Pavithra <meetpavithramsc@gmail.com> wrote:
Dear Dr. Elaine,
Thank you for the reply. I tried to report the bug before I mailed this group. To be exact for the past two days, I tried to report the bug. But, It didn't work. The preference I was talking about is the "web access" in which i changed the http proxy true and tried. I have tried Fetching pdb, Emdb, which was successful. But, with uniprot I'm getting the previously mentioned error. I have tried different uniprot Ids but I get the same error.
On Thu, Oct 24, 2013 at 10:18 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Pavithra, I can't reproduce this problem -- the fetch of UniProt oprd_human is successful for me in Chimera 1.7 and newer versions of Chimera. I don't know what preference you are talking about... if you meant the download directory, that only specifies a local directory for saving the files and should not have "http" in it.
In general, you should report problems using the Chimera menu: Help... Report a Bug instead of sending email to this address. In the report form, you can include a description of what you did and your email (if you want feedback). Some other things to try and maybe mention in the report: can you fetch anything from UniProt? Can you fetch anything from any database (PDB, etc.)? Thanks 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 Oct 23, 2013, at 6:01 PM, Pavithra wrote:
Dear chimera users,
I'm trying comparative modeling tutorial in chimera tutorials and I'm getting the following error in using fetch uniprot id.
Steps followed: Menu--> fetch by ID--> selected uniprot--> "oprd_human" "P41143" (tried all combinations)
Error:
BadStatusLine: ''
File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status raise BadStatusLine(line)
See reply log for Python traceback.
I tried changing the preference to use "http" but nothing fix it. please help.
-- regards, Pavithra.K.B. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- regards, Pavithra.K.B. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Pavithra