Discussion group for the ARIA software

["Kelly, Mark" <Mark.Kelly AT ucsf.edu>]

Hi Vicky/All,

we have been running our calculations in ARIA vers 2.3.1. If we want to take advantage of the log harmonic potential should we use 2.3.2 or is this only important for the adaptive violation tolerance (below)? Would we need different parameters for using just the log harmonic potential in 2.31, than those from Mareuil et. al., 2015) for the adaptive violation tolerance incorporated in 2.3.2. The linux workstation James is using has 2.3.1 that comes with SBGrid. I have a 2.3.2 version on my Mac I can try.

Thanks for all your help,

Mark   

The latest version (2.3.2)

The source code of version 2.3 is available as a tarball: aria2.3.tar.gz

• Version 2.3.2 updates version 2.31 and  offers several new features:

• compatibility with CCPNmr Analsyis 2.4
• new PDF reports
• improved Zinc ions patches
• Constraints combination
• Automatic superimposition of best structures and bundle RMSD
• Adaptive violation tolerance (cf Mareuil et al. J Bio NMR 015)
• various fixes
  

• ARIA version 2.3 requires the python module numpy (Numeric not supported)

 

Past versions

Version 2.3.1

The source code of version 2.3 is available as a tarball: aria2.3.tar.gz

• Version 2.3 is based on the ARIA software library.
• Version 2.3 is an extension of the version 2.2 of the program. It offers several new features:

• extension of support for symmetric oligomers (C3, C5 and D2 symmetries)
• compatibility with CCPNmr version 2 (version 1 not supported)
• improved import/export of CCPN data (eg. import of structure models, NMR Calculation runs in Analysis...)
• introduction of a log-harmonic potential for distance restraints (Nilges et al. Structure, 2008)
• support for coordinated zinc ions
• automated Molprobilty clashlist analysis
• partial support for solid-state NMR through CCPN Distance constraint lists (see Note)

• ARIA version 2.3 requires the python module numpy (Numeric not supported)

NB : The log-harmonic potential requires to recompile CNS with the sources provided in the aria archive (See README or installation notes)

On Jun 2, 2020, at 11:41 PM, Higman, Vicky (Dr.) <vad5 AT LEICESTER.AC.UK> wrote:

Hi Mark,

try using the parameters suggested in table S5 in the supplementary info of the Mareuil et al. 2015 paper. I have generally had good experiences with that. Note in particular the number of SA high temp and cooling steps - these are much larger than what is typically used.

All the best,

Vicky

---

From: aria-discuss-request AT services.cnrs.fr <aria-discuss-request AT services.cnrs.fr> on behalf of Kelly, Mark <Mark.Kelly AT ucsf.edu>
Sent: 02 June 2020 18:17
To: aria-discuss AT services.cnrs.fr <aria-discuss AT services.cnrs.fr>
Cc: Benjamin Bardiaux <bardiaux AT pasteur.fr>; Longbotham, James <James.Longbotham AT ucsf.edu>
Subject: Re: [aria-discuss] Next step in calculations

 

Hello All,

we switched ‘on’ the log harmonic potential, but now our structures don’t look very nice. I wonder if we did not set the parameters correctly or do we have to switch something else off?

Best,

Mark

<logharmonic_potential enabled="yes" use_auto_weight="yes" weight_unambig="1.0" weight_ambig="1.0" weight_hbond="1.0"/>

On Apr 29, 2020, at 10:50 AM, Kelly, Mark <Mark.Kelly AT ucsf.edu> wrote:

Hello All,

we tried to restart a run that had been successful before and get the error below - would anyone have a suggestion what might be wrong?

hope all are safe and well,

Mark

Begin forwarded message:

From: "Longbotham, James" <James.Longbotham AT ucsf.edu>

Subject: RE: Next step in calculations

Date: April 29, 2020 at 10:37:57 AM PDT

To: "Kelly, Mark" <Mark.Kelly AT ucsf.edu>

Ok so that last run I  described below failed. I thought it ould have something to do with the merged restraint lists so I tried to run it again with the restraints I used previously (before assignment) and it failed still! See error below. Not sure what’s going on

 

Exception in thread Thread-1:

Traceback (most recent call last):

  File "/programs/x86_64-linux/ccpnmr/2.4.2/python2.7/lib/python2.7/threading.py", line 810, in __bootstrap_inner

    self.run()

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/JobManager.py", line 193, in run

    f(self)

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/JobManager.py", line 331, in job_done

    self.dispatch_job(host)

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/JobManager.py", line 337, in dispatch_job

    self.done()

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/JobManager.py", line 384, in done

    self.__callback()

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/cns.py", line 2662, in <lambda>

    callback = lambda v = vars, f = self.refine_done: f(v)

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/cns.py", line 2522, in refine_done

    self.__callback()

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/Protocol.py", line 654, in <lambda>

    c = self.structure_calc_done: c(engine, molecule, it)

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/Protocol.py", line 624, in structure_calc_done

    ensemble = engine.getEnsemble(it_settings, molecule)

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/cns.py", line 666, in getEnsemble

    ensemble.read(pdbfiles, molecule, float_files = swapped_atoms)

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/StructureEnsemble.py", line 194, in read

    pdb_dict = self.reader.read(files[j], chain_types, format[j])

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/PDBReader.py", line 186, in read

   dict['noe_violations'] = float(data[13:].split(',')[0])

ValueError: could not convert string to float: D1_ApoH3_violations_1.pdb"