Discussion group for the ARIA software

[Umit Akbey <umitakbey AT gmail.com>]

Benjamin maybe its not a bad idea to upload a "youtube" video on these things, apparently there are many little questions/points when one tries.

You can be pretty famous & liked as a youtuber scientist.

Have a tought 

Cheerd

Umit

-------- Original message --------

From: Benjamin Bardiaux <bardiaux AT pasteur.fr>

Date: 6/11/20 14:26 (GMT+01:00)

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

Cc: 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

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
---------------------------------------------