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Re: [aria-discuss] Mareuil et. al., J Bio NMR 2015 in ARIA 2.3.2 Problem


Chronological Thread  
  • From: Benjamin Bardiaux <bardiaux AT pasteur.fr>
  • To: "Kelly, Mark" <Mark.Kelly AT ucsf.edu>
  • Cc: "aria-discuss AT services.cnrs.fr" <aria-discuss AT services.cnrs.fr>, "Longbotham, James" <James.Longbotham AT ucsf.edu>
  • Subject: Re: [aria-discuss] Mareuil et. al., J Bio NMR 2015 in ARIA 2.3.2 Problem
  • Date: Thu, 11 Jun 2020 14:26:20 +0200
  • Ironport-sdr: SQfqNTNT8YALDsE1qkzL89xcqnB4vZNV7a46fcPvdONVcdfkmVGKukiSXZgrO653d06j7Oqp6n TM4H9XBVDP+g==
  • Organization: CNRS

Hi Mark,

I think I now have them set to the values in Table S5 now (see below)? Sigma_mode should be ‘*auto*’ correct?

Correct.


Do I also need to change the Force field values for:

Bond and improper angles (50 kcal/mol/Rad^2) and H vdW radii for H-H interactions (1.0/1.2 A)?

if so - where do I do that?

It's done when choosing parallhdg5.3softbig.pro as parameter set.

<parameter_definition name="parallhdg5.3softbig.pro" filename="”/>

Best,

Benjamin


Thanks for all your help,

Mark



<violation_analysis sigma_mode="auto" violation_tolerance="200.0" violation_threshold="0.5"/>
      <violation_analysis sigma_mode="auto" violation_tolerance="6.0" violation_threshold="0.5"/>
      <violation_analysis sigma_mode="auto" violation_tolerance="3.0" violation_threshold="0.5"/>
      <violation_analysis sigma_mode="auto" violation_tolerance="2.0" violation_threshold="0.5"/>
      <violation_analysis sigma_mode="auto" violation_tolerance="1.0" violation_threshold="0.5"/>
      <violation_analysis sigma_mode="auto" violation_tolerance="1.0" violation_threshold="0.5"/>
      <violation_analysis sigma_mode="auto" violation_tolerance="0.5" violation_threshold="0.5"/>
      <violation_analysis sigma_mode="auto" violation_tolerance="0.5" violation_threshold="0.5"/>
      <violation_analysis sigma_mode="auto" violation_tolerance="0.5" violation_threshold="0.5"/>

On Jun 10, 2020, at 12:54 AM, Benjamin Bardiaux <bardiaux AT PASTEUR.FR <mailto:bardiaux AT PASTEUR.FR>> wrote:

Hi Mark,

Did you also change the violation_tolerance parameter for every iteration using the values from Supp. Table S5 of Mareuil et. al., J Bio NMR 2015 ?

We will do our best to try and make it easier to choose this protocol in the ARIA project/GUI.

Best,

Benjamin

On 10/06/2020 05:12, Kelly, Mark wrote:
Dear All,
I wanted to run the protocol of Mareuil et. al., J Bio NMR 2015 in ARIA 2.3.2 (including that of Nilges et, al., Structure 2008 and earlier papers).
I made the following changes to my ARIA project.xml file (at the bottom), but when I run the calculation the structures improve in the first iterations, but then in spite of there being apparently only a few violations the number of noes used suddenly goes down by about 1/2?
any ideas what might be wrong?
Thanks,
Fitted:
## Backbone (N,CA,C,O) : 1.06 +/- 0.22 A
## Backbone (N,CA,C,O) : 1.04 +/- 0.24 A
## Backbone (N,CA,C,O) : 0.92 +/- 0.16 A
## Backbone (N,CA,C,O) : 0.89 +/- 0.21 A
## Backbone (N,CA,C,O) : 0.83 +/- 0.21 A
## Backbone (N,CA,C,O) : 0.86 +/- 0.17 A
## Backbone (N,CA,C,O) : 1.59 +/- 0.32 A
## Backbone (N,CA,C,O) : 1.80 +/- 0.48 A
## Backbone (N,CA,C,O) : 1.78 +/- 0.25 A
## Backbone (N,CA,C,O) : 1.90 +/- 0.34 A
## Used during calculation: 1988
## Used during calculation: 1988
## Used during calculation: 1921
## Used during calculation: 1443
## Used during calculation: 1449
## Used during calculation: 1450
## Used during calculation: 595
## Used during calculation: 624
## Used during calculation: 634
## Violated:                0 (0.0)
## Violated:                0 (0.0)
## Violated:                4 (0.2)
## Violated:                17 (1.2)
## Violated:                6 (0.4)
## Violated:                3 (0.2)
## Violated:                60 (10.1)
## Violated:                43 (6.9)
## Violated:                39 (6.2)
*Changes to ARIA project.xml file:*
(1) the softening of the force field:
<parameter_definition name="parallhdg5.3softbig.pro" filename="”/>
(2) log harmonic potential, Bayesian weighting of distance restraints (?) and increased number of steps (table S5 in the supplementary):
<logharmonic_potential enabled="yes" use_auto_weight="yes" weight_unambig="25.0" weight_ambig="25.0" weight_hbond="25.0"/>
      </annealing_parameters>
      <md_parameters dynamics="torsion" random_seed="12468759" tad_temp_high="10000.0" tad_timestep_factor="9.0" cartesian_temp_high="2000.0" cartesian_first_iteration="0" timestep="0.002" temp_cool1_final="1000.0" temp_cool2_final="50.0" steps_high="20000" steps_refine="4000" steps_cool1="30000" steps_cool2="30000"/>
(3) a procedure that automatically adjusts the violation tolerance used in the selection of active restraints (?):
<violation_analysis sigma_mode="auto" violation_tolerance="0.1" violation_threshold="0.5"/>
We used distance restraints file from ccpn:
<unambiguous_distance_restraints file="" format="ccpn" ccpn_id="18|5" enabled="yes" add_to_network="no" calibrate="all_iterations_except_first" run_network_anchoring="no" filter_contributions="yes"/>
<ambiguous_distance_restraints file="" format="ccpn" ccpn_id="18|6" enabled="yes" add_to_network="no" calibrate="all_iterations_except_first" run_network_anchoring="no" filter_contributions="yes”/>
Do we need to specify lower/upper bounds with the restraints?
<lower_bound_correction value="0.0" enabled="no"/>
<upper_bound_correction value="6.0" enabled="no"/>
On Jun 4, 2020, at 10:18 AM, Kelly, Mark <Mark.Kelly AT ucsf.edu <mailto:Mark.Kelly AT ucsf.edu> <mailto:Mark.Kelly AT ucsf.edu>> wrote:


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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__aria.pasteur.fr_archives_aria2.3.2.tar.gz&d=DwMGaQ&c=iORugZls2LlYyCAZRB3XLg&r=298wo5FTw8hoVM2Z8-GREvQZopmfLGcC8YyMqGWWpmw&m=ylym3D2tfYPSSGTR-dqOKNPR0CkS38Jx05ca3cwk4X0&s=qHozzh-zB6f9WIwHHU4etIB9GRxLgtVnrq-lW_pLIsg&e=>

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

     o compatibility with CCPNmr Analsyis 2.4
     o new PDF reports
     o improved Zinc ions patches
     o Constraints combination
     o Automatic superimposition of best structures and bundle RMSD
     o *Adaptive violation tolerance (cf Mareuil et al. J Bio NMR 015)*
     o 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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__aria.pasteur.fr_archives_aria2.3.1.tar.gz&d=DwMGaQ&c=iORugZls2LlYyCAZRB3XLg&r=298wo5FTw8hoVM2Z8-GREvQZopmfLGcC8YyMqGWWpmw&m=ylym3D2tfYPSSGTR-dqOKNPR0CkS38Jx05ca3cwk4X0&s=92BqyQFaDa94JaW0RW5wvF7MpnMXpjbYFnan014NksM&e=>

*
   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:

     o extension of support for symmetric oligomers (C3, C5 and D2 symmetries)
     o compatibility with *CCPNmr version 2* (version 1 not supported)
     o improved import/export of CCPN data (eg. import of structure models,
       NMR Calculation runs in Analysis...)
     o *introduction of a log-harmonic potential for distance restraints
       (Nilges /et al./ Structure, 2008)*
     o support for coordinated *zinc* ions
     o automated Molprobilty /clashlist /analysis
     o /partial support for solid-state NMR through CCPN Distance constraint
       lists (see Note
       
<https://urldefense.proofpoint.com/v2/url?u=http-3A__aria.pasteur.fr_documentation_tutorials_aria-2Dand-2Dccpn&d=DwMGaQ&c=iORugZls2LlYyCAZRB3XLg&r=298wo5FTw8hoVM2Z8-GREvQZopmfLGcC8YyMqGWWpmw&m=ylym3D2tfYPSSGTR-dqOKNPR0CkS38Jx05ca3cwk4X0&s=HoVS4Ts4MXRPLmKdp7XZlOoP7Efp947r1QvuaD3LCzI&e=>)/

 * 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) <https://urldefense.proofpoint.com/v2/url?u=http-3A__aria.pasteur.fr_downloads_installation-2Dnotes&d=DwMGaQ&c=iORugZls2LlYyCAZRB3XLg&r=298wo5FTw8hoVM2Z8-GREvQZopmfLGcC8YyMqGWWpmw&m=ylym3D2tfYPSSGTR-dqOKNPR0CkS38Jx05ca3cwk4X0&s=AkyNVlkWK6pyCEhHSCSKtdk7uQfN9DZhDpoNVkXf9Vg&e=>/



On Jun 2, 2020, at 11:41 PM, Higman, Vicky (Dr.) <vad5 AT LEICESTER.AC.UK <mailto:vad5 AT LEICESTER.AC.UK> <mailto: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 <mailto:aria-discuss-request AT services.cnrs.fr> <mailto:aria-discuss-request AT services.cnrs.fr><aria-discuss-request AT services.cnrs.fr <mailto:aria-discuss-request AT services.cnrs.fr> <mailto:aria-discuss-request AT services.cnrs.fr>> on behalf of Kelly, Mark <Mark.Kelly AT ucsf.edu <mailto:Mark.Kelly AT ucsf.edu> <mailto:Mark.Kelly AT ucsf.edu>>
*Sent:*02 June 2020 18:17
*To:*aria-discuss AT services.cnrs.fr <mailto:aria-discuss AT services.cnrs.fr> <mailto:aria-discuss AT services.cnrs.fr><aria-discuss AT services.cnrs.fr <mailto:aria-discuss AT services.cnrs.fr> <mailto:aria-discuss AT services.cnrs.fr>>
*Cc:*Benjamin Bardiaux <bardiaux AT pasteur.fr <mailto:bardiaux AT pasteur.fr> <mailto:bardiaux AT pasteur.fr>>; Longbotham, James <James.Longbotham AT ucsf.edu <mailto:James.Longbotham AT ucsf.edu> <mailto: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 <mailto:Mark.Kelly AT ucsf.edu> <mailto: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 <mailto:James.Longbotham AT ucsf.edu> <mailto: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 <mailto:Mark.Kelly AT ucsf.edu> <mailto: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"


--
---------------------------------------------
Dr Benjamin Bardiaux bardiaux AT pasteur.fr <mailto:bardiaux AT pasteur.fr>
Unité de Bioinformatique Structurale
CNRS UMR3528 - Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
---------------------------------------------



--
---------------------------------------------
Dr Benjamin Bardiaux bardiaux AT pasteur.fr
Unité de Bioinformatique Structurale
CNRS UMR3528 - Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
---------------------------------------------



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