Discussion group for the ARIA software

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

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.