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Hello Helene--
> Your suggestion did work well. All energies are OK now (except the ones
> for RDCs), no message about a "cycle link", but ... the calculation stop,
> after having written the violations file for structure 0.
>
> Here is the error message:
>
> Traceback (most recent call last):
> File "<string>", line 2, in <module>
> File "/PROG/LINUX/prog/Xplor-NIH/xplor-nih-2.26/python/trace.py", line
> 180, in run
> exec cmd in dict, dict
> File "<string>", line 1, in <module>
> File "refinementSchwieters.py", line 385, in <module>
> averageCompSel="not resname ANI and not name H*" ).run()
> File
> "/PROG/LINUX/prog/Xplor-NIH/xplor-nih-2.26/python/simulationTools.py",
> li ne 281, in run
> s.structLoopAction(s)
> File "refinementSchwieters.py", line 366, in calcOneStructure
> loopInfo.writeStructure(potList)
> File
> "/PROG/LINUX/prog/Xplor-NIH/xplor-nih-2.26/python/simulationTools.py",
> li ne 626, in writeStructure
> user = pwd.getpwuid(os.geteuid())[0]
> KeyError: 'getpwuid(): uid not found: 1137'
> PyInterp::command: error executing: >execfile('refinementSchwieters.py')<
>
Unfortunately, I didn't catch that exception type (for whatever reason
the computer you ran on doesn't have complete or consistent user id
info). My apologies.
The fix is simple, requiring that the file python/simulationTools.py
must be replaced or patched. I have placed a fixed version on the
Xplor-NIH updates page:
http://nmr.cit.nih.gov/xplor-nih/updates/current/
This is fixed for version 2.27 and might possibly cause problems for
2.26 (which you're running). Alternatively, you can apply the simple
patch shown below.
best regards--
Charles
*** python/simulationTools.py 2010-10-04 21:01:55 +0000
- --- python/simulationTools.py 2011-01-20 18:19:00 +0000
***************
*** 624,630 ****
user="unknown"
try:
user = pwd.getpwuid(os.geteuid())[0]
! except IndexError:
from os import environ
try:
user = environ["LOGNAME"]
- --- 624,630 ----
user="unknown"
try:
user = pwd.getpwuid(os.geteuid())[0]
! except (IndexError,KeyError):
from os import environ
try:
user = environ["LOGNAME"]
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