Discussion group for the ARIA software

[Benjamin Bardiaux <bardiaux AT pasteur.fr>]

Dear Mark, dear list,

It seems like it's the first case of distance restraints from CCPN made from 
peaks with negative height/intensity.
We simply forgot to anticipate that...

The current version of aria2.3.2 has been fixed, so we invite users to update their version by downloading the latest 
sources at http://aria.pasteur.fr/archives/aria2.3.2.tar.gz

Sorry for that.

Best,

Benjamin


On 15/09/2021 18:18, Kelly, Mark wrote:
> Dear ARIA List,
>
>
> I tried using the CCPN - Analysis Network Anchoring function to make ’Network 
> Anchored’ restraints (Structure: Make Distance Restraints) and and used these 
> to calculate in ARIA. I spit these into umambig (29|1) and ambig restraints 
> (29|2). Then I used these restraints I generated in Analysis (v2.4.2) to 
> calculate in ARIA. The first iteration in ARIA completes ok, but then I get 
> errors (see below). When I look at the refine.out I see errors and missing 
> atom coordinates:
>
> [TomCatVI:~/H3_StructCalc/aria_temp.tmpc4H4nT1631659131/run_cns_1] markkelly% 
> grep ERR refine.out
> ERROR: matrix is not a rotation matrix
> ERROR: matrix is not a rotation matrix
> ERROR: matrix is not a rotation matrix
> ERROR: matrix is not a rotation matrix
> ERROR: matrix is not a rotation matrix
> ERROR: matrix is not a rotation matrix
> ERROR: matrix is not a rotation matrix
> ERROR: matrix is not a rotation matrix
> ERROR: matrix is not a rotation matrix
> ERROR: matrix is not a rotation matrix
> ERROR: matrix is not a rotation matrix
>
> The first iteration (it0) completes just fine and the structures look pretty 
> good for it0 and have quite low energies (7,000 total) - which is nice. It 
> seems to be when ARIA prepares to run the next iteration (it1) and starts to 
> (re-)calibrate the Umambig restraints that an invalid value is calculated for 
> the power factor (below). It doesn’t seem to have a problem with the ambig 
> restraints.
>
> Any ideas?
>
> Best and stay safe,
>
> Mark
>
>
> MESSAGE [CNS]: Template PDB-file has been created.
> MESSAGE [Project]: Starting ARIA main protocol on Tue Sep 14 15:30:39 2021
> MESSAGE [Project]: -------------------- Assigning spectra --------------------
> MESSAGE [Protocol]: ---------------------- Iteration 0 -----------------------
>
> MESSAGE [Protocol]: Calibrating spectrum "Unambig 29|1"...
> MESSAGE [Protocol]: Calibrating spectrum "Ambig 29|2"...
> MESSAGE [Job]: Starting job: "cd 
> /Users/markkelly/H3_StructCalc/aria_temp.tmpQ0p
>                Nxf1631658629/run_cns_2; csh -f /Users/markkelly/H3_StructCalc/
>                aria_temp.tmpQ0pNxf1631658629/run_cns_2/refine.csh &"MESSAGE 
> [Protocol]: Waiting for completion of structure calculation...
>
> MESSAGE [Job]: Job "cd 
> /Users/markkelly/H3_StructCalc/aria_temp.tmpQ0pNxf1631658
>                629/run_cns_2; csh -f 
> /Users/markkelly/H3_StructCalc/aria_temp.tm
>                pQ0pNxf1631658629/run_cns_2/refine.csh &" completed.
> MESSAGE [Job]: Starting job: "cd 
> /Users/markkelly/H3_StructCalc/aria_temp.tmpQ0p
>                Nxf1631658629/run_cns_1; csh -f /Users/markkelly/H3_StructCalc/
>                aria_temp.tmpQ0pNxf1631658629/run_cns_1/refine.csh &"
> MESSAGE [Job]: Job "cd 
> /Users/markkelly/H3_StructCalc/aria_temp.tmpQ0pNxf1631658
>                629/run_cns_1; csh -f 
> /Users/markkelly/H3_StructCalc/aria_temp.tm
>                pQ0pNxf1631658629/run_cns_1/refine.csh &" completed.
> MESSAGE [CNS]: CNS output files have been copied to 
> /Users/markkelly/H3_StructCa
>                lc/run45/structures/it0/cns
> MESSAGE [Protocol]: Structure calculation done.
> MESSAGE [StructureEnsemble]: Reading PDB files ...
> MESSAGE [StructureEnsemble]: PDB files read.
> MESSAGE [CNS]: 2 PDB-files and float-files read.
> MESSAGE [CNS]: 
> /Users/markkelly/H3_StructCalc/run45/structures/it0/H3_091421_AR_
>                45_1.float: 111 atom pairs swapped
> MESSAGE [CNS]: 
> /Users/markkelly/H3_StructCalc/run45/structures/it0/H3_091421_AR_
>                45_2.float: 96 atom pairs swapped
> MESSAGE [Protocol]: Iteration 0 done.
> MESSAGE [Protocol]: ---------------------- Iteration 1 -----------------------
>
> MESSAGE [Protocol]: Calibrating spectrum "Unambig 29|1"...
> /Applications/aria2.3.2/src/py/aria/Protocol.py:1487: RuntimeWarning: invalid 
> value encountered in power
>   factor = power(factor, 1./6)
> /Applications/aria2.3.2/src/py/aria/Protocol.py:1510: RuntimeWarning: invalid 
> value encountered in power
>   distances = factor * power(peak_sizes, -1. / 6)
> /Applications/aria2.3.2/src/py/aria/ViolationAnalyser.py:251: RuntimeWarning: 
> invalid value encountered in less
>   violated_lower = less(d_avg, lower - tol)
> /Applications/aria2.3.2/src/py/aria/ViolationAnalyser.py:252: RuntimeWarning: 
> invalid value encountered in greater
>   violated_upper = greater(d_avg, upper + tol)
> MESSAGE [Protocol]: Violation analysis done: 0 / 1258 restraints (0.0 %)
>                     violated.
> MESSAGE [Protocol]: Calibrating spectrum "Ambig 29|2"...
> MESSAGE [Protocol]: Violation analysis done: 0 / 224 restraints (0.0 %)
>                     violated.
> MESSAGE [Job]: Starting job: "cd 
> /Users/markkelly/H3_StructCalc/aria_temp.tmpQ0p
>                Nxf1631658629/run_cns_2; csh -f /Users/markkelly/H3_StructCalc/
>                aria_temp.tmpQ0pNxf1631658629/run_cns_2/refine.csh &"
> MESSAGE [Protocol]: Performing analysis on calculated structures...
> MESSAGE [Protocol]: Analysis done.
> MESSAGE [Protocol]: NOE-restaint list (text) written (/Users/markkelly/
>                     H3_StructCalc/run45/structures/it0/noe_restraints).
> MESSAGE [Protocol]: Report for Merging-step written (/Users/markkelly/
>                     H3_StructCalc/run45/structures/it0/noe_restraints.merged).
> MESSAGE [Protocol]: Waiting for completion of structure calculation...
> MESSAGE [Job]: Job "cd 
> /Users/markkelly/H3_StructCalc/aria_temp.tmpQ0pNxf1631658
>                629/run_cns_2; csh -f 
> /Users/markkelly/H3_StructCalc/aria_temp.tm
>                pQ0pNxf1631658629/run_cns_2/refine.csh &" completed.
> MESSAGE [Job]: Starting job: "cd 
> /Users/markkelly/H3_StructCalc/aria_temp.tmpQ0p
>                Nxf1631658629/run_cns_1; csh -f /Users/markkelly/H3_StructCalc/
>                aria_temp.tmpQ0pNxf1631658629/run_cns_1/refine.csh &"
> MESSAGE [Job]: Job "cd 
> /Users/markkelly/H3_StructCalc/aria_temp.tmpQ0pNxf1631658
>                629/run_cns_1; csh -f 
> /Users/markkelly/H3_StructCalc/aria_temp.tm
>                pQ0pNxf1631658629/run_cns_1/refine.csh &" completed.
> MESSAGE [CNS]: CNS output files have been copied to 
> /Users/markkelly/H3_StructCa
>                lc/run45/structures/it1/cns
> MESSAGE [Job manager]: shutdown.
> Traceback (most recent call last):
>   File "/Applications/aria2.3.2/aria2.py", line 903, in <module>
>     verbose_level, use_condor=condor)
>   File "/Applications/aria2.3.2/aria2.py", line 813, in run_aria
>     project.go(use_condor)
>   File "/Applications/aria2.3.2/src/py/aria/Project.py", line 1666, in go
>     self.run_protocol(first_iteration)
>   File "/Applications/aria2.3.2/src/py/aria/Project.py", line 1672, in 
> run_protocol
>     last_iteration = self.getProtocol().go(iteration, self.getMolecule())
>   File "/Applications/aria2.3.2/src/py/aria/Protocol.py", line 1841, in go
>     iteration = self.start(iteration, molecule)
>   File "/Applications/aria2.3.2/src/py/aria/Protocol.py", line 1825, in start
>     return self.run_protocol(molecule, iteration)
>   File "/Applications/aria2.3.2/src/py/aria/Protocol.py", line 2300, in 
> run_protocol
>     is_first_it)
>   File "/Applications/aria2.3.2/src/py/aria/Protocol.py", line 2255, in 
> run_iteration
>     self.error(StandardError, err_msg)
>   File "/Applications/aria2.3.2/src/py/aria/ariabase.py", line 211, in error
>     raise exception, msg
> StandardError: USER ERROR <aria.Protocol.Protocol> File 
> "/Applications/aria2.3.2/src/py/aria/Protocol.py", line 2300 in run_protocol
> Structure calculation failed for structure 1.
> Structure calculation failed for structure 2.
> Please check your setup and the CNS output files for errors.


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