SASREF problem in SASPy

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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Pernille
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Posts: 12
Joined: 2013.09.24 14:57

SASREF problem in SASPy

#1 Post by Pernille » 2017.12.05 13:58

Hi
I am trying to model a protein hexamer from three dimers using sasref but running through pymol the program keep crashing with following error msg:

Exception in thread sasref_thread:
Traceback (most recent call last):
File "C:\ProgramData\PyMOL\lib\threading.py", line 801, in __bootstrap_inner
self.run()
File "C:\ProgramData\PyMOL\lib\threading.py", line 754, in run
self.__target(*self.__args, **self.__kwargs)
File "C:\ProgramData\PyMOL\lib\site-packages\pmg_tk\startup\saspy.py", line 1128, in sasref
systemCommand(['sasref'], stdin=commandfile)
File "C:\ProgramData\PyMOL\lib\site-packages\pmg_tk\startup\saspy.py", line 626, in systemCommand
status = subprocess.call(command, **kwargs)
File "C:\ProgramData\PyMOL\lib\subprocess.py", line 168, in call
return Popen(*popenargs, **kwargs).wait()
File "C:\ProgramData\PyMOL\lib\subprocess.py", line 382, in __init__
errread, errwrite), to_close = self._get_handles(stdin, stdout, stderr)
File "C:\ProgramData\PyMOL\lib\subprocess.py", line 532, in _get_handles
c2pwrite = self._make_inheritable(c2pwrite)
File "C:\ProgramData\PyMOL\lib\subprocess.py", line 566, in _make_inheritable
_subprocess.DUPLICATE_SAME_ACCESS)
WindowsError: [Error 6] The handle is invalid

I have tried with the same data using the commandline version of sasref which works.
Crysol, alpraxin and sreflex is working so it does not seem to be the plugin. I have the latest Atsas and Pymol (licensed) installments.

Best regards
Pernille

sasha
Active member
Posts: 46
Joined: 2014.03.05 17:56

Re: SASREF problem in SASPy

#2 Post by sasha » 2017.12.06 00:15

Dear Pernille,

Thanks for reporting this. Please install an updated SASpy for ATSAS 2.8.2 from (right-click, save as...):
https://raw.githubusercontent.com/embls ... r/saspy.py

the problem should be fixed in that version, if not, please let me know.

Best,

sasha

sasha
Active member
Posts: 46
Joined: 2014.03.05 17:56

Re: SASREF problem in SASPy

#3 Post by sasha » 2017.12.18 12:42

Dear Pernille,

the issue was deeper in the Pyhon libraries that PyMOL 2.0 is using in Windows, now I found a workaround by calling SASREF with a different function.
Please download the updated github version (for ATSAS 2.8.3), it should work properly:
https://raw.githubusercontent.com/embls ... r/saspy.py

Best,

sasha

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