[PyMOL] Still need help with fetch and pymol 1.7
I am posting this again as I have still not figured out why I am unable to fetch or use the pdb plugin loader with pymol 1.7 I have cut/copied/pasted the error msg I get below. I have tried uninstalling and reinstalling python 2.7.6 as well as python 1.7 (I have windows 64 bit --so I tried the 64 bit version 1st, and when that did not work I unindtalled adn then re-installed using the windows 32 bit version. (I prev had pymol 1.3 but uninstalled that as well). This forum has been a great source of help for my before so hope yoiu guys can help again! Thank you. PyMOLfetch 4bd2 please wait ... Exception in thread Thread-4: Traceback (most recent call last): File C:\Python27\lib\threading.py, line 810, in __bootstrap_inner self.run() File C:\Python27\lib\threading.py, line 763, in run self.__target(*self.__args, **self.__kwargs) File C:\Python27\lib\site-packages\pymol\commanding.py, line 561, in wrapper func(*args, **kwargs) File C:\Python27\lib\site-packages\pymol\importing.py, line 1348, in _multifetch discrete, multiplex, zoom, type, path, file, quiet, _self) File C:\Python27\lib\site-packages\pymol\importing.py, line 1292, in _fetch contents = internal.file_read(url) File C:\Python27\lib\site-packages\pymol\internal.py, line 308, in file_read handle = urllib.urlopen(finfo) File C:\Python27\lib\urllib2.py, line 127, in urlopen return _opener.open(url, data, timeout) File C:\Python27\lib\urllib2.py, line 404, in open response = self._open(req, data) File C:\Python27\lib\urllib2.py, line 422, in _open '_open', req) File C:\Python27\lib\urllib2.py, line 382, in _call_chain result = func(*args) File C:\Python27\lib\urllib2.py, line 1403, in ftp_open mtype = mimetypes.guess_type(req.get_full_url())[0] File C:\Python27\lib\mimetypes.py, line 297, in guess_type init() File C:\Python27\lib\mimetypes.py, line 358, in init db.read_windows_registry() File C:\Python27\lib\mimetypes.py, line 258, in read_windows_registry for subkeyname in enum_types(hkcr): File C:\Python27\lib\mimetypes.py, line 249, in enum_types ctype = ctype.encode(default_encoding) # omit in 3.x! UnicodeDecodeError: 'ascii' codec can't decode byte 0xd7 in position 2: ordinal not in range(128) -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Still need help with fetch and pymol 1.7
I think there's a bug in python's code, not pymol's In the file that it describes at the end ( C:\Python27\lib\mimetypes.py ) , you should change line 250 from: except UnicodeEncodeError: to except (UnicodeEncodeError,UnicodeDecodeError): keeping the indentation in the file and so on. Then the code will skip the entries in the windows registry that are causing issues. -David On Mon, Jan 20, 2014 at 8:40 AM, Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edu wrote: I am posting this again as I have still not figured out why I am unable to fetch or use the pdb plugin loader with pymol 1.7 I have cut/copied/pasted the error msg I get below. I have tried uninstalling and reinstalling python 2.7.6 as well as python 1.7 (I have windows 64 bit --so I tried the 64 bit version 1st, and when that did not work I unindtalled adn then re-installed using the windows 32 bit version. (I prev had pymol 1.3 but uninstalled that as well). This forum has been a great source of help for my before so hope yoiu guys can help again! Thank you. PyMOLfetch 4bd2 please wait ... Exception in thread Thread-4: Traceback (most recent call last): File C:\Python27\lib\threading.py, line 810, in __bootstrap_inner self.run() File C:\Python27\lib\threading.py, line 763, in run self.__target(*self.__args, **self.__kwargs) File C:\Python27\lib\site-packages\pymol\commanding.py, line 561, in wrapper func(*args, **kwargs) File C:\Python27\lib\site-packages\pymol\importing.py, line 1348, in _multifetch discrete, multiplex, zoom, type, path, file, quiet, _self) File C:\Python27\lib\site-packages\pymol\importing.py, line 1292, in _fetch contents = internal.file_read(url) File C:\Python27\lib\site-packages\pymol\internal.py, line 308, in file_read handle = urllib.urlopen(finfo) File C:\Python27\lib\urllib2.py, line 127, in urlopen return _opener.open(url, data, timeout) File C:\Python27\lib\urllib2.py, line 404, in open response = self._open(req, data) File C:\Python27\lib\urllib2.py, line 422, in _open '_open', req) File C:\Python27\lib\urllib2.py, line 382, in _call_chain result = func(*args) File C:\Python27\lib\urllib2.py, line 1403, in ftp_open mtype = mimetypes.guess_type(req.get_full_url())[0] File C:\Python27\lib\mimetypes.py, line 297, in guess_type init() File C:\Python27\lib\mimetypes.py, line 358, in init db.read_windows_registry() File C:\Python27\lib\mimetypes.py, line 258, in read_windows_registry for subkeyname in enum_types(hkcr): File C:\Python27\lib\mimetypes.py, line 249, in enum_types ctype = ctype.encode(default_encoding) # omit in 3.x! UnicodeDecodeError: 'ascii' codec can't decode byte 0xd7 in position 2: ordinal not in range(128) -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Still need help with fetch and pymol 1.7
Thank you thank you! I will try that later today--I do appreciate the help. Did I say thank you yet? Suzanne From: David Hall [li...@cowsandmilk.net] Sent: Monday, January 20, 2014 8:34 AM To: Lapolla, Suzanne M (HSC) Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Still need help with fetch and pymol 1.7 I think there's a bug in python's code, not pymol's In the file that it describes at the end ( C:\Python27\lib\mimetypes.py ) , you should change line 250 from: except UnicodeEncodeError: to except (UnicodeEncodeError,UnicodeDecodeError): keeping the indentation in the file and so on. Then the code will skip the entries in the windows registry that are causing issues. -David On Mon, Jan 20, 2014 at 8:40 AM, Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edumailto:suzanne-lapo...@ouhsc.edu wrote: I am posting this again as I have still not figured out why I am unable to fetch or use the pdb plugin loader with pymol 1.7 I have cut/copied/pasted the error msg I get below. I have tried uninstalling and reinstalling python 2.7.6 as well as python 1.7 (I have windows 64 bit --so I tried the 64 bit version 1st, and when that did not work I unindtalled adn then re-installed using the windows 32 bit version. (I prev had pymol 1.3 but uninstalled that as well). This forum has been a great source of help for my before so hope yoiu guys can help again! Thank you. PyMOLfetch 4bd2 please wait ... Exception in thread Thread-4: Traceback (most recent call last): File C:\Python27\lib\threading.py, line 810, in __bootstrap_inner self.run() File C:\Python27\lib\threading.py, line 763, in run self.__target(*self.__args, **self.__kwargs) File C:\Python27\lib\site-packages\pymol\commanding.py, line 561, in wrapper func(*args, **kwargs) File C:\Python27\lib\site-packages\pymol\importing.py, line 1348, in _multifetch discrete, multiplex, zoom, type, path, file, quiet, _self) File C:\Python27\lib\site-packages\pymol\importing.py, line 1292, in _fetch contents = internal.file_read(url) File C:\Python27\lib\site-packages\pymol\internal.py, line 308, in file_read handle = urllib.urlopen(finfo) File C:\Python27\lib\urllib2.py, line 127, in urlopen return _opener.open(url, data, timeout) File C:\Python27\lib\urllib2.py, line 404, in open response = self._open(req, data) File C:\Python27\lib\urllib2.py, line 422, in _open '_open', req) File C:\Python27\lib\urllib2.py, line 382, in _call_chain result = func(*args) File C:\Python27\lib\urllib2.py, line 1403, in ftp_open mtype = mimetypes.guess_type(req.get_full_url())[0] File C:\Python27\lib\mimetypes.py, line 297, in guess_type init() File C:\Python27\lib\mimetypes.py, line 358, in init db.read_windows_registry() File C:\Python27\lib\mimetypes.py, line 258, in read_windows_registry for subkeyname in enum_types(hkcr): File C:\Python27\lib\mimetypes.py, line 249, in enum_types ctype = ctype.encode(default_encoding) # omit in 3.x! UnicodeDecodeError: 'ascii' codec can't decode byte 0xd7 in position 2: ordinal not in range(128) -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrkhttps://urldefense.proofpoint.com/v1/url?u=http://pubads.g.doubleclick.net/gampad/clk?id%3D119420431%26iu%3D/4140/ostg.clktrkk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=uQj%2BLzvmZqzzizFwe1YvZKDZZUpHplHD8opYqcvhAn8%3D%0As=c39cf5d893b52e6f5ec16a6387487a94fd5de5b59cd6b95a0d25cf1c90af7cc7 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto:PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-usershttps://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/pymol-usersk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=uQj%2BLzvmZqzzizFwe1YvZKDZZUpHplHD8opYqcvhAn8%3D%0As=08fff961e62c1cc1f73daa6de0c230f296af4fc761099414b802108d56d83777 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.nethttps://urldefense.proofpoint.com/v1/url?u=http://www.mail-archive.com/pymol-users%40lists.sourceforge.netk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=uQj%2BLzvmZqzzizFwe1YvZKDZZUpHplHD8opYqcvhAn8%3D%0As=382ddb0abe1d34e33a3163ac0bece11503526da3ed8cf39e505f0b5afc0a1802 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads
Re: [PyMOL] Still need help with fetch and pymol 1.7
Just wanted to say that your fix did solve my problem. Thanks again! From: David Hall [li...@cowsandmilk.net] Sent: Monday, January 20, 2014 8:34 AM To: Lapolla, Suzanne M (HSC) Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Still need help with fetch and pymol 1.7 I think there's a bug in python's code, not pymol's In the file that it describes at the end ( C:\Python27\lib\mimetypes.py ) , you should change line 250 from: except UnicodeEncodeError: to except (UnicodeEncodeError,UnicodeDecodeError): keeping the indentation in the file and so on. Then the code will skip the entries in the windows registry that are causing issues. -David On Mon, Jan 20, 2014 at 8:40 AM, Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edumailto:suzanne-lapo...@ouhsc.edu wrote: I am posting this again as I have still not figured out why I am unable to fetch or use the pdb plugin loader with pymol 1.7 I have cut/copied/pasted the error msg I get below. I have tried uninstalling and reinstalling python 2.7.6 as well as python 1.7 (I have windows 64 bit --so I tried the 64 bit version 1st, and when that did not work I unindtalled adn then re-installed using the windows 32 bit version. (I prev had pymol 1.3 but uninstalled that as well). This forum has been a great source of help for my before so hope yoiu guys can help again! Thank you. PyMOLfetch 4bd2 please wait ... Exception in thread Thread-4: Traceback (most recent call last): File C:\Python27\lib\threading.py, line 810, in __bootstrap_inner self.run() File C:\Python27\lib\threading.py, line 763, in run self.__target(*self.__args, **self.__kwargs) File C:\Python27\lib\site-packages\pymol\commanding.py, line 561, in wrapper func(*args, **kwargs) File C:\Python27\lib\site-packages\pymol\importing.py, line 1348, in _multifetch discrete, multiplex, zoom, type, path, file, quiet, _self) File C:\Python27\lib\site-packages\pymol\importing.py, line 1292, in _fetch contents = internal.file_read(url) File C:\Python27\lib\site-packages\pymol\internal.py, line 308, in file_read handle = urllib.urlopen(finfo) File C:\Python27\lib\urllib2.py, line 127, in urlopen return _opener.open(url, data, timeout) File C:\Python27\lib\urllib2.py, line 404, in open response = self._open(req, data) File C:\Python27\lib\urllib2.py, line 422, in _open '_open', req) File C:\Python27\lib\urllib2.py, line 382, in _call_chain result = func(*args) File C:\Python27\lib\urllib2.py, line 1403, in ftp_open mtype = mimetypes.guess_type(req.get_full_url())[0] File C:\Python27\lib\mimetypes.py, line 297, in guess_type init() File C:\Python27\lib\mimetypes.py, line 358, in init db.read_windows_registry() File C:\Python27\lib\mimetypes.py, line 258, in read_windows_registry for subkeyname in enum_types(hkcr): File C:\Python27\lib\mimetypes.py, line 249, in enum_types ctype = ctype.encode(default_encoding) # omit in 3.x! UnicodeDecodeError: 'ascii' codec can't decode byte 0xd7 in position 2: ordinal not in range(128) -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrkhttps://urldefense.proofpoint.com/v1/url?u=http://pubads.g.doubleclick.net/gampad/clk?id%3D119420431%26iu%3D/4140/ostg.clktrkk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=uQj%2BLzvmZqzzizFwe1YvZKDZZUpHplHD8opYqcvhAn8%3D%0As=c39cf5d893b52e6f5ec16a6387487a94fd5de5b59cd6b95a0d25cf1c90af7cc7 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto:PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-usershttps://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/pymol-usersk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=uQj%2BLzvmZqzzizFwe1YvZKDZZUpHplHD8opYqcvhAn8%3D%0As=08fff961e62c1cc1f73daa6de0c230f296af4fc761099414b802108d56d83777 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.nethttps://urldefense.proofpoint.com/v1/url?u=http://www.mail-archive.com/pymol-users%40lists.sourceforge.netk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=uQj%2BLzvmZqzzizFwe1YvZKDZZUpHplHD8opYqcvhAn8%3D%0As=382ddb0abe1d34e33a3163ac0bece11503526da3ed8cf39e505f0b5afc0a1802 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments
