SAXS

Small Angle X-ray Scattering Initiative for Europe :: Forum
It is currently 2018.01.24 08:00

All times are UTC + 2 hours




Post new topic Reply to topic  [ 3 posts ] 
Author Message
 Post subject: SASREF problem in SASPy
PostPosted: 2017.12.05 13:58 
Offline
Member

Joined: 2013.09.24 14:57
Posts: 12
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


Top
 Profile  
 
PostPosted: 2017.12.06 00:15 
Offline
Active member

Joined: 2014.03.05 17:56
Posts: 43
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/emblsaxs/saspy/master/saspy.py

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

Best,

sasha


Top
 Profile  
 
PostPosted: 2017.12.18 12:42 
Offline
Active member

Joined: 2014.03.05 17:56
Posts: 43
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


Top
 Profile  
 
Display posts from previous:  Sort by  
Post new topic Reply to topic  [ 3 posts ] 

All times are UTC + 2 hours


Who is online

Users browsing this forum: No registered users and 1 guest


You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot post attachments in this forum

Search for:
Jump to:  
cron
Powered by phpBB® Forum Software © phpBB Group