Hey Paul,
I’ve attached a copy of the log after opening up coot. There is an error in
there but not sure what it means.
IOError: [Errno socket error] [Errno 10061] No connection could be made because
the target machine actively refused it
Cheers,
Sam
From: Paul Emsley <[email protected]>
Sent: 04 June 2020 11:46
To: Horrell, Sam (DLSLtd,RAL,LSCI) <[email protected]>
Subject: Re: [ccp4bb] Coot CCP4i2 extensions
Coot should write a log somewhere - not sure where it is - and that will record
problems reading startup scripts. If you can find it it might be useful.
Paul.
On 04/06/2020 11:43, Horrell, Sam (DLSLtd,RAL,LSCI) wrote:
Hi Stuart,
Thanks for the reply, I am running on a windows 10 machine so maybe it’s OS
specific.
I went to the file menu and it no longer has the save mol to ccp4i2 option. I
have tried rebooting, rolling back the update, reinstalling the update and
nothing has changed I’m afraid. The full path to the coot executable in the
preferences is blank but if there was a problem I don’t think coot would have
loaded at all from the interface.
Cheers,
Sam
From: Stuart McNicholas
<[email protected]><mailto:[email protected]>
Sent: 04 June 2020 11:38
To: Horrell, Sam (DLSLtd,RAL,LSCI)
<[email protected]><mailto:[email protected]>
Cc: [email protected]<mailto:[email protected]>
Subject: Re: [ccp4bb] Coot CCP4i2 extensions
Dear Sam,
Apologies for your problem. I have tested myself on Mac and do not see the
problem, however I will try on Linux and Windows as well.
However, this menu not functioning may not mean that you cannot saves. Do "Save
mol to CCP4i2.." and "Save to CCP4i2" appear in Coot's File menu? If so you can
use those. If not, then you do indeed still have a problem. One simple thought
might be to reboot, if you have not already done so. Clearly Coot is, for some
reason, not able to communicate properly. A reboot might help.
Best wishes,
Stuart
On Thu, 4 Jun 2020 at 10:57, Horrell, Sam (DLSLtd,RAL,LSCI)
<[email protected]<mailto:[email protected]>> wrote:
Hello CCP4bb,
I just installed the latest update and it seems to have a problem with Coot’s
CCP4i2 extensions.
The dropdown menu no longer appears when clicked so it’s impossible to save to
the i2 gui.
I’ve rolled back the update but the bug is still present.
Cheers,
Sam
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INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON:
C:\CCP4-7\7.1\lib\data\monomers\
INFO:: Reading coordinate file:
C:\CCP4-7\WinCoot\share\coot\standard-residues.pdb
PDB file C:\CCP4-7\WinCoot\share\coot\standard-residues.pdb has been read.
Spacegroup: P 1
initalize graphics molecules...done.
filter_fileselection_filenames_state ()
get_active_map_drag_flag ()
use_graphics_interface_state ()
INFO:: coot.py imported
INFO:: coot_python initialized
Running python script
C:/CCP4-7/WinCoot/python27/lib/site-packages/coot/coot_load_modules.py
Good Morning Zoi74479, Welcome to Coot version 0.8.9.2
set_display_intro_string ("Good Morning Zoi74479, Welcome to Coot version
0.8.9.2")
Coot Python Scripting GUI code found and loaded.
Coot Python Scripting GUI code found and loaded.
use_graphics_interface_state ()
Running python script C:/CCP4-7/WinCoot/.coot-preferences/coot_toolbuttons.py
Running python script
C:/CCP4-7/WinCoot/.coot-preferences/template_key_bindings.py
Running python script C:/CCP4-7/WinCoot/.coot-preferences/xenops_symmetry.py
set_show_symmetry_master (1)
filter_fileselection_filenames_state ()
get_active_map_drag_flag ()
INFO:: There are 1 command line scripts to run
C:\Users\zoi74479\CCP4I2_PROJECTS\MPRO_Z369936976\CCP4_JOBS\job_47\script.py
Running python script
C:/Users/zoi74479/CCP4I2_PROJECTS/MPRO_Z369936976/CCP4_JOBS/job_47/script.py
Managed to load ccp4i2CootInterface
** Drop directory for output files is
C:\Users\zoi74479\CCP4I2_PROJECTS\MPRO_Z369936976\CCP4_JOBS\job_47\COOT_FILE_DROP
** CCP4I2_HTTP_PORT is 43434
** CCP4I2_PROJECT_NAME is
MPRO_Z369936976
** CCP4I2_PROJECT_ID is
22118200a3f111ea9dfa50e085dbce72
(<module 'wrappers.coot_rebuild.script.ccp4i2CootInterface' from
'C:\CCP4-7\7.1\share\ccp4i2\wrappers\coot_rebuild\script\ccp4i2CootInterface.pyc'>,
<wrappers.coot_rebuild.script.ccp4i2CootInterface.ccp4i2CootInterface instance
at 0x28C686E8>)
[Errno socket error] timed out
handle_read_draw_molecule_with_recentre
("C:\Users\zoi74479\CCP4I2_PROJECTS\MPRO_Z369936976\CCP4_JOBS\job_46\46_mpro_z369936976_xyzout_prosmart_refmac.pdb",
1)
INFO:: Reading coordinate file:
C:\Users\zoi74479\CCP4I2_PROJECTS\MPRO_Z369936976\CCP4_JOBS\job_46\46_mpro_z369936976_xyzout_prosmart_refmac.pdb
PDB file
C:\Users\zoi74479\CCP4I2_PROJECTS\MPRO_Z369936976\CCP4_JOBS\job_46\46_mpro_z369936976_xyzout_prosmart_refmac.pdb
has been read.
Spacegroup: I 1 2 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 0 read successfully
DEBUG:: there were 0 types with no dictionary
Error [Errno socket error] [Errno 10061] No connection could be made because
the target machine actively refused it loading coordinates
C:\Users\zoi74479\CCP4I2_PROJECTS\MPRO_Z369936976\CCP4_JOBS\job_46\46_mpro_z369936976_xyzout_prosmart_refmac.pdb
make_and_draw_map
("C:\Users\zoi74479\CCP4I2_PROJECTS\MPRO_Z369936976\CCP4_JOBS\job_46\46_mpro_z369936976_fphiout_prosmart_refmac.mtz",
"F", "PHI", "PHI", 0, 0)
INFO:: making map from mtz filename
C:\Users\zoi74479\CCP4I2_PROJECTS\MPRO_Z369936976\CCP4_JOBS\job_46\46_mpro_z369936976_fphiout_prosmart_refmac.mtz
INFO:: Number of observed reflections: 6660
INFO:: finding ASU unique map points with sampling rate 1.8
INFO:: grid sampling...Nuvw = ( 60, 72, 160)
INFO:: 0.014 seconds to read MTZ file
INFO:: 0.017 seconds to initialize map
INFO:: 0.01 seconds for FFT
INFO:: 0.013 seconds for statistics
Map mean: ........ -2.90556e-005
Map sigma: ....... 0.213489
Map maximum: ..... 1.18001
Map minimum: ..... -0.770868
INFO:: 0.041 seconds for contour map
INFO:: 0.095 seconds in total
make_and_draw_map
("C:\Users\zoi74479\CCP4I2_PROJECTS\MPRO_Z369936976\CCP4_JOBS\job_46\46_mpro_z369936976_diffphiout_prosmart_refmac.mtz",
"F", "PHI", "PHI", 0, 1)
INFO:: making map from mtz filename
C:\Users\zoi74479\CCP4I2_PROJECTS\MPRO_Z369936976\CCP4_JOBS\job_46\46_mpro_z369936976_diffphiout_prosmart_refmac.mtz
INFO:: Number of observed reflections: 6660
INFO:: finding ASU unique map points with sampling rate 1.8
INFO:: grid sampling...Nuvw = ( 60, 72, 160)
INFO:: 0.009 seconds to read MTZ file
INFO:: 0.025 seconds to initialize map
INFO:: 0.006 seconds for FFT
INFO:: 0.018 seconds for statistics
Map mean: ........ -1.01205e-005
Map sigma: ....... 0.0678231
Map maximum: ..... 0.297126
Map minimum: ..... -0.335837
INFO:: 0.039 seconds for contour map
INFO:: 0.097 seconds in total
Traceback (most recent call last):
File
"C:\CCP4-7\7.1\share\ccp4i2\wrappers\coot_rebuild\script\ccp4i2CootInterface.py",
line 84, in populateMenus
projectList = self.performDatabaseLookup('listProjects')
File
"C:\CCP4-7\7.1\share\ccp4i2\wrappers\coot_rebuild\script\ccp4i2CootInterface.py",
line 226, in performDatabaseLookup
json = urllib.urlopen(url,proxies={}).read()
File "C:\CCP4-7\WinCoot\python27\lib\urllib.py", line 87, in urlopen
return opener.open(url)
File "C:\CCP4-7\WinCoot\python27\lib\urllib.py", line 213, in open
return getattr(self, name)(url)
File "C:\CCP4-7\WinCoot\python27\lib\urllib.py", line 350, in open_http
h.endheaders(data)
File "C:\CCP4-7\WinCoot\python27\lib\httplib.py", line 1038, in endheaders
self._send_output(message_body)
File "C:\CCP4-7\WinCoot\python27\lib\httplib.py", line 882, in _send_output
self.send(msg)
File "C:\CCP4-7\WinCoot\python27\lib\httplib.py", line 844, in send
self.connect()
File "C:\CCP4-7\WinCoot\python27\lib\httplib.py", line 821, in connect
self.timeout, self.source_address)
File "C:\CCP4-7\WinCoot\python27\lib\socket.py", line 575, in
create_connection
raise err
IOError: [Errno socket error] [Errno 10061] No connection could be made because
the target machine actively refused it
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