Hi Guys,
Thank you very much for your prompt help and great effort! It seems that ccpnmr and aria are working together.
Thank you!!!
Best regards,
Xuehui
--------------------------------------------
On Mon, 10/26/15, Xue Liu <[log in to unmask]> wrote:
Subject: Re: Aria2.3 not working with ccpnmr2.4.2
To: [log in to unmask]
Date: Monday, October 26, 2015, 9:32 AM
Hi
Wayne,I still
can not get them to work. Could I downgrade to some older
ccpnmr version to run aria2? If so, which version do you
recommand? 2.3.1?Thank you
very much!
Best
regards,Xuehui
On Friday, October 23, 2015 6:57 PM,
Wayne Boucher <[log in to unmask]> wrote:
Hello,
I’ve backtracked the
Analysis 2.4.2 code to use the old-fashioned if statement
syntax, so hopefully that will work with Python 2.5 now
(there are a couple of other occurrences of the newer syntax
in the 2.4.2 code but hopefully in files that Aria does not
directly or indirectly import, otherwise I’ll have to
change those as well).
Wayne
> On 23 Oct
2015, at 01:35, Xue Liu <[log in to unmask]>
wrote:
>
> Dear
Benjamin:
>
> Still
can not get it to work. I used the python in ccpnmr
directory to start aria2.py with -g option and get the
following message:
>
> ARIA Version 2.3.1. Authors: Benjamin
Bardiaux, Michael Habeck, Jens Linge,
>
Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping,
and Michael Nilges.
>
> If you use this software, please quote the
following reference(s):
>
> Rieping W., Habeck M., Bardiaux B.,
Bernard A., Malliavin T.E.,
> Nilges
M.(2007) ARIA2: automated NOE assignment and data
integration in NMR
> structure
calculation. Bioinformatics 23:381-382
>
> Segmentation fault
>
> Should I update the
system's python to 2.7?
>
> Regards,
>
> Xuehui
>
>
>
--------------------------------------------
> On Thu, 10/22/15, Benjamin Bardiaux <[log in to unmask]>
wrote:
>
> Subject:
Re: Aria2.3 not working with ccpnmr2.4.2
> To: [log in to unmask]
> Date: Thursday, October 22, 2015, 4:35
PM
>
> Dear
Xuehui,
>
> Try
running aria2.3 with
> python >= 2.5
(best is to use the same python
> as
ccpnmr)
>
>
Regards,
>
>
Benjamin
>
> On
> 10/22/15 9:55 AM, Xue Liu wrote:
>>
> Hello,
>> I could not get aria2.3 work
> with ccpnmr anymore which was fine months
ago.
>> Since I haven't been using
the aria
> for a while, the only thing I
remembered is that I upgraded
> the
ccpnmr someday. I did whatever I could and still could
> not get aria2.3 to work. I've noticed
that while
> ccpnmr2.4.1 use python2.6,
2.4.2 is using python2.7 now.
> Could
this be the cause of the problem? Or should I download
> the whole 2.4.2 package rather than
upgrade from 2.4.1?
> Thank you very much
for any advice!
>>
>> Here is the error:
>>
> Loading project
"run.xml"...
>>
> MESSAGE [Project]: Temporary directory has
been set to
> /home/xhliu/Data/
>>
>
>
Projects/mry_N2_20151022/aria_temp.tmpgVhg0Y1445500714
>> MESSAGE [Project]: List of
available
> machines is empty. Running
calculations on
>>
> localhost
"localhost.localdomain",
>
assuming 1 CPU. Using /
>>
> usr/bin/cns as
structure
> engine.
>> MESSAGE [Project]: Checking
> host list ...
>>
MESSAGE [Job manager]:
> Command
"csh -f" ... ok.
>>
> MESSAGE [Project]: Cache is disabled.
>>
> Model read
finished. Duration 2.40438103676
>>
Model validity check skipped
>>
MESSAGE [Project]: ------------ Reading
>
data from CCPN data model ------------
>>
> MESSAGE
[Project]: Opening CCPN data model
>
"/home/xhliu/Data/Projects/
>>
>
> mry_N2_20151022"...
>>
> MESSAGE
[Project]: CCPN data model opened.
>>
MESSAGE [Project]: Retrieving molecular
>
system "MS1", chain code(s) "A"...
>> MESSAGE [Project]: Retrieving peak
list
> "(project=defaultProject,
experiment=2,
>>
> data_source=1,
serial=1)", shift list
>
"1" ...
>> Traceback
(most
> recent call last):
>> File
>
"/home/xhliu/programs/aria2.3/aria2.py", line
903,
> in ?
>>
verbose_level,
>
use_condor=condor)
>> File
>
"/home/xhliu/programs/aria2.3/aria2.py", line
811,
> in run_aria
>>
>
project.load_and_preprocess_data()
>>
> File
>
"/home/xhliu/programs/aria2.3/src/py/aria/Project.py",
> line 1426, in load_and_preprocess_data
>> self.read_data()
>> File
>
"/home/xhliu/programs/aria2.3/src/py/aria/Project.py",
> line 1186, in read_data
>>
>
self.read_ccpn_data()
>> File
>
"/home/xhliu/programs/aria2.3/src/py/aria/Project.py",
> line 709, in read_ccpn_data
>>
> from
aria.exportToCcpn import getAriaRun
>> File
>
"/home/xhliu/programs/aria2.3/src/py/aria/exportToCcpn.py",
> line 1, in ?
>>
from
>
ccpnmr.analysis.core.ConstraintBasic import
> makeNmrConstraintStore,
makeStructureGeneration,
>
getFixedResonance
>> File
>
"/home/xhliu/programs/ccpnmr/ccpnmr2.4/python/ccpnmr/analysis/core/ConstraintBasic.py",
> line 1637
>>
minFreq =
> expDimRef.minAliasedFreq if
expDimRef.minAliasedFreq is not
> None
else valRange[0]
>>
>
^
>> SyntaxError: invalid
syntax
>>
>>
>>
> Best,
>>
>>
> Xuehui
>>
>
>
> --
>
---------------------------------------------
> Dr Benjamin Bardiaux [log in to unmask]
> Unité de Bioinformatique Structurale
> CNRS UMR3528 - Institut Pasteur
> 25,28 rue du Docteur Roux 75015 Paris,
> France
>
---------------------------------------------
|