Re: [ccp4bb] problems with running PARROT
Hmm - that looks almost too good - Mask volumes are expected to be less than 1.. NCS operator statistics: Operator_number Mask_volume/ASU Correlation 11.0010.911 20.9980.912 30.9540.863 40.8880.854 And the rotation angles etc look as though chains A B C & D could be symmetry euivalents? rotation ~ 90 0 180 - ie a crystallographic two fold Are you sure you arent giving PARROT a model with actual symmetry equivalent molecules? Eleanor On Fri, 25 Jun 2021 at 14:38, Savvas Savvides wrote: > There you go Eleanor > > Best wishes, — Savvas > > > > > # Task 41 parrot running cparrot > # Mini-MTZ input to HKLIN: > # Data type parameter jobannotation > # Reflections F_SIGF 39 il_phaser.1.259: NULL_dname > imported by job 39 > # Phases ABCD 39 il_phaser.1.259: NULL_dname > imported by job 39 > mtzin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz > colin-fo F_SIGF_F,F_SIGF_SIGF > colin-phifom ABCD_PHI,ABCD_FOM > seqin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/seqin.fasta > pdbin-mr > /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb > mtzout /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklout.mtz > xmlout /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/program.xml > cycles 3 > anisotropy-correction > solvent-content 0.6 > ncs-mask-filter-radius 20.0 > > > > > > > ### > ### > ### > ### CCP4 7.1.014: cparrotversion 1.0.6 : 20/04/21## > ### > User: root Run date: 25/ 6/2021 Run time: 12:41:49 > > > Please reference: Collaborative Computational Project, Number 4. 2011. > "Overview of the CCP4 suite and current developments". Acta Cryst. D67, > 235-242. > as well as any specific reference in the program write-up. > > > > Copyright 2008-2010 Kevin Cowtan and University of York. > > > $TEXT:Reference: $$ Please reference $$ > > 'Recent developments in classical density modification.' > Cowtan K. (2010) Acta Cryst. D66, 470-478. > > $$ > > mtzin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz > colin-fo F_SIGF_F,F_SIGF_SIGF > colin-phifom ABCD_PHI,ABCD_FOM > seqin > /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/seqin.fasta > pdbin-mr > /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb > mtzout/Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklout.mtz > xmlout > /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/program.xml > cycles3 > anisotropy-correction > solvent-content 0.6 > ncs-mask-filter-radius20.0 > > > PDB file: > /Applications/ccp4-7.1/lib/data/reference_structures/reference-1tqw.pdb > Number of atoms read: 9432 > PDB file: > /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb > Number of atoms read: 7264 > > MTZ file: /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz > Number of reflections: 22867Number of columns: 7 > > Applying anisotropy correction: > | -0.05391, 8.59e-17,0.1649| > | 8.59e-17, -0.1351, -3.06e-17| > |0.1649, -3.06e-17, -0.5043| > > NCS from atomic model: > > NCS operator found relating chains A and B > Polar rotation/deg: 89.9215,-0.233543,179.754 > Euler rotation/deg: -57.6965,179.708,122.771 > Source: xyz = (-5.624, 9.951, 36.36) > Target: xyz = (-5.528, 38.96, 64.43) > > NCS operator found relating chains B and A > Polar rotation/deg: 90.0785,179.766,179.754 > Euler rotation/deg: 57.2294,179.708,-122.303 > Source: xyz = (-5.528, 38.96, 64.43) > Target: xyz = (-5.624, 9.951, 36.36) > > NCS operator found relating chains C and D > Polar rotation/deg: 90.1347,-0.132348,178.552 > Euler rotation/deg: -100.677,178.528,79.5875 > Source: xyz = (-17.66, 33.01, 93.38) > Target: xyz = (-17.88, 16.06, 7.398) > > NCS operator found relating chains D and C > Polar rotation/deg: 89.8653,179.868,178.552 > Euler rotation/deg: 100.412,178.528,-79.3228 > Source: xyz = (-17.88, 16.06, 7.398) > Target: xyz = (-17.66, 33.01, 93.38) > > > -- Cycle: 1 > > Suggested radius for solvent mask determination: 5.68666 > > NCS operator: 1 > NCS masking: Mask volume as fraction of ASU: 1.00 Multiplicity: 10 > Contiguity score: 1.000 Self-overlap score: 0.151 > NXop refinement- correlation before: 0.539, after: 0.581 > NXop old: -57.7 179.7 122.8 -5.6 10.0 36.4 -5.5 39.0 64.4 >
Re: [ccp4bb] problems with running PARROT
There you go Eleanor Best wishes, — Savvas # Task 41 parrot running cparrot # Mini-MTZ input to HKLIN: # Data type parameter jobannotation # Reflections F_SIGF 39 il_phaser.1.259: NULL_dname imported by job 39 # Phases ABCD 39 il_phaser.1.259: NULL_dname imported by job 39 mtzin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz colin-fo F_SIGF_F,F_SIGF_SIGF colin-phifom ABCD_PHI,ABCD_FOM seqin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/seqin.fasta pdbin-mr /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb mtzout /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklout.mtz xmlout /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/program.xml cycles 3 anisotropy-correction solvent-content 0.6 ncs-mask-filter-radius 20.0 ### ### ### ### CCP4 7.1.014: cparrotversion 1.0.6 : 20/04/21## ### User: root Run date: 25/ 6/2021 Run time: 12:41:49 Please reference: Collaborative Computational Project, Number 4. 2011. "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242. as well as any specific reference in the program write-up. Copyright 2008-2010 Kevin Cowtan and University of York. $TEXT:Reference: $$ Please reference $$ 'Recent developments in classical density modification.' Cowtan K. (2010) Acta Cryst. D66, 470-478. $$ mtzin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz colin-foF_SIGF_F,F_SIGF_SIGF colin-phifomABCD_PHI,ABCD_FOM seqin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/seqin.fasta pdbin-mr /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb mtzout /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklout.mtz xmlout /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/program.xml cycles 3 anisotropy-correction solvent-content 0.6 ncs-mask-filter-radius 20.0 PDB file: /Applications/ccp4-7.1/lib/data/reference_structures/reference-1tqw.pdb Number of atoms read: 9432 PDB file: /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb Number of atoms read: 7264 MTZ file: /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz Number of reflections: 22867Number of columns: 7 Applying anisotropy correction: | -0.05391, 8.59e-17,0.1649| | 8.59e-17, -0.1351, -3.06e-17| |0.1649, -3.06e-17, -0.5043| NCS from atomic model: NCS operator found relating chains A and B Polar rotation/deg: 89.9215,-0.233543,179.754 Euler rotation/deg: -57.6965,179.708,122.771 Source: xyz = (-5.624, 9.951, 36.36) Target: xyz = (-5.528, 38.96, 64.43) NCS operator found relating chains B and A Polar rotation/deg: 90.0785,179.766,179.754 Euler rotation/deg: 57.2294,179.708,-122.303 Source: xyz = (-5.528, 38.96, 64.43) Target: xyz = (-5.624, 9.951, 36.36) NCS operator found relating chains C and D Polar rotation/deg: 90.1347,-0.132348,178.552 Euler rotation/deg: -100.677,178.528,79.5875 Source: xyz = (-17.66, 33.01, 93.38) Target: xyz = (-17.88, 16.06, 7.398) NCS operator found relating chains D and C Polar rotation/deg: 89.8653,179.868,178.552 Euler rotation/deg: 100.412,178.528,-79.3228 Source: xyz = (-17.88, 16.06, 7.398) Target: xyz = (-17.66, 33.01, 93.38) -- Cycle: 1 Suggested radius for solvent mask determination: 5.68666 NCS operator: 1 NCS masking: Mask volume as fraction of ASU: 1.00 Multiplicity: 10 Contiguity score: 1.000 Self-overlap score: 0.151 NXop refinement- correlation before: 0.539, after: 0.581 NXop old: -57.7 179.7 122.8 -5.6 10.0 36.4 -5.5 39.0 64.4 NXop new: 105.8 180.0 -74.1 -7.4 11.2 40.1 -7.3 37.8 60.9 NCS operator: 2 NCS masking: Mask volume as fraction of ASU: 1.00 Multiplicity: 10 Contiguity score: 1.000 Self-overlap score: 0.154 NXop refinement- correlation before: 0.528, after: 0.577 NXop old: 57.2 179.7 -122.3 -5.5 39.0 64.4 -5.6 10.0 36.4 NXop new: -94.6 179.8 85.4 -3.8 36.5 60.3 -3.8 12.5 40.6 NCS operator: 3 NCS masking: Mask volume as fraction of ASU: 0.95 Multiplicity: 9 Contiguity score: 0.999 Self-overlap score: 0.149 NXop refinement- correlation before: 0.447, after: 0.606 NXop old: -100.7 178.5 79.6-17.7 33.0 93.4-17.9 16.17.4 NXop new: -140.4 179.8 39.7 -9.8 36.7 79.4 -9.9 12.4 21.6 NCS operator:
Re: [ccp4bb] problems with running PARROT
The extract from the log file looks OK - can you send the whole log.txt? Eleanor On Fri, 25 Jun 2021 at 12:09, Savvas Savvides wrote: > Dear colleagues, > > I am trying to run Parrot via CCP4-7.1.014 and the CCP4i2 GUI on a > MacBookPro (OSX 10.15.7) and keep getting the following error report as the > program is in the process of outputting SigmaA statistics. > > Below, I provide two pieces of information: > (1) The Error message > (2) The last page of the ouput file where the program ends up crashing > with the error message. > > Thank you in advance for any insights/input on this issue. > > Best wishes, > Savvas > > > > > > > Error Report for Job 41: Density modification - PARROT > > -ERROR- CTaskParrot:9 Error in wrapper parrot 0.0:: Failed starting external > process > > - this can be due to a number of things, but usually is due to the command > used by subprocess/QProcess not working for some reason. > > Missing input files, bad commands, non-functional programs etc. Check log > files and stdout. > Process: cparrot > > -ERROR- CTaskParrot:47 Error in wrapper parrot 0.0:: Error in checking > external process after completion > exit status and code: -11 -11 > > > > ——— > > -- Cycle: 1 > > Suggested radius for solvent mask determination: 5.68666 > > NCS operator: 1 > NCS masking: Mask volume as fraction of ASU: 1.00 Multiplicity: 10 > Contiguity score: 1.000 Self-overlap score: 0.151 > NXop refinement- correlation before: 0.539, after: 0.581 > NXop old: -57.7 179.7 122.8 -5.6 10.0 36.4 -5.5 39.0 64.4 > NXop new: 105.8 180.0 -74.1 -7.4 11.2 40.1 -7.3 37.8 60.9 > > NCS operator: 2 > NCS masking: Mask volume as fraction of ASU: 1.00 Multiplicity: 10 > Contiguity score: 1.000 Self-overlap score: 0.154 > NXop refinement- correlation before: 0.528, after: 0.577 > NXop old: 57.2 179.7 -122.3 -5.5 39.0 64.4 -5.6 10.0 36.4 > NXop new: -94.6 179.8 85.4 -3.8 36.5 60.3 -3.8 12.5 40.6 > > NCS operator: 3 > NCS masking: Mask volume as fraction of ASU: 0.95 Multiplicity: 9 > Contiguity score: 0.999 Self-overlap score: 0.149 > NXop refinement- correlation before: 0.447, after: 0.606 > NXop old: -100.7 178.5 79.6-17.7 33.0 93.4-17.9 16.17.4 > NXop new: -140.4 179.8 39.7 -9.8 36.7 79.4 -9.9 12.4 21.6 > > NCS operator: 4 > NCS masking: Mask volume as fraction of ASU: 0.89 Multiplicity: 9 > Contiguity score: 0.998 Self-overlap score: 0.179 > NXop refinement- correlation before: 0.423, after: 0.588 > NXop old: 100.4 178.5 -79.3-17.9 16.17.4-17.7 33.0 93.4 > NXop new: 144.0 179.8 -36.0-24.0 11.7 20.5-23.7 37.5 80.6 > > > NCS operator statistics: > Operator_number Mask_volume/ASU Correlation > 11.0010.911 > 20.9980.912 > 30.9540.863 > 40.8880.854 > > > $TABLE :Cycle 1 Electron density histograms: > $GRAPHS :Protein:N:1,4,5,6::Solvent:N:1,7,8::Simulation:N:1,3,4: $$ > rho_min rho_max Simulatn P_init P_trgt P_mod S_init S_mod $$ > $$ > -0.317 -0.282 0.000 0.000 0.017 0.008 0.000 0.000 > -0.282 -0.247 0.000 0.000 0.026 0.014 0.000 0.000 > -0.247 -0.212 0.002 0.002 0.036 0.024 0.000 0.000 > -0.212 -0.177 0.007 0.007 0.045 0.039 0.000 0.000 > -0.177 -0.143 0.022 0.019 0.057 0.056 0.003 0.000 > -0.143 -0.108 0.050 0.048 0.064 0.076 0.020 0.000 > -0.108 -0.073 0.093 0.094 0.071 0.081 0.069 0.000 > -0.073 -0.038 0.142 0.147 0.070 0.090 0.156 0.000 > -0.038 -0.003 0.172 0.175 0.072 0.091 0.234 0.000 > -0.003 0.032 0.172 0.173 0.068 0.085 0.237 1.000 > 0.032 0.067 0.141 0.141 0.063 0.075 0.167 0.000 > 0.067 0.101 0.099 0.094 0.057 0.071 0.080 0.000 > 0.101 0.136 0.056 0.053 0.053 0.063 0.026 0.000 > 0.136 0.171 0.029 0.026 0.049 0.053 0.006 0.000 > 0.171 0.206 0.011 0.012 0.044 0.048 0.001 0.000 > 0.206 0.241 0.004 0.005 0.038 0.038 0.000 0.000 > 0.241 0.276 0.001 0.002 0.033 0.033 0.000 0.000 > 0.276 0.311 0.000 0.001 0.030 0.025 0.000 0.000 > 0.311 0.345 0.000 0.000 0.025 0.016 0.000 0.000 > 0.345 0.380 0.000 0.000 0.021 0.014 0.000 0.000 > $$ > > > Gamma 0.24162 > > Log likelihood: 2.920853e+04 Log likelihood (free): 0.00e+00 > > $TABLE :Cycle 1 SigmaA statistics: > $GRAPHS :SigmaA statistics:N:1,2,3: $$ > 1/resol^2 sigmaA(s) sigmaA(w) $$ > $$ > 0.012 0.682 0.675 > 0.025 0.629 0.635 > 0.035 0.659 0.664 > 0.043
[ccp4bb] problems with running PARROT
Dear colleagues, I am trying to run Parrot via CCP4-7.1.014 and the CCP4i2 GUI on a MacBookPro (OSX 10.15.7) and keep getting the following error report as the program is in the process of outputting SigmaA statistics. Below, I provide two pieces of information: (1) The Error message (2) The last page of the ouput file where the program ends up crashing with the error message. Thank you in advance for any insights/input on this issue. Best wishes, Savvas Error Report for Job 41: Density modification - PARROT -ERROR- CTaskParrot:9 Error in wrapper parrot 0.0:: Failed starting external process - this can be due to a number of things, but usually is due to the command used by subprocess/QProcess not working for some reason. Missing input files, bad commands, non-functional programs etc. Check log files and stdout. Process: cparrot -ERROR- CTaskParrot:47 Error in wrapper parrot 0.0:: Error in checking external process after completion exit status and code: -11 -11 ——— -- Cycle: 1 Suggested radius for solvent mask determination: 5.68666 NCS operator: 1 NCS masking: Mask volume as fraction of ASU: 1.00 Multiplicity: 10 Contiguity score: 1.000 Self-overlap score: 0.151 NXop refinement- correlation before: 0.539, after: 0.581 NXop old: -57.7 179.7 122.8 -5.6 10.0 36.4 -5.5 39.0 64.4 NXop new: 105.8 180.0 -74.1 -7.4 11.2 40.1 -7.3 37.8 60.9 NCS operator: 2 NCS masking: Mask volume as fraction of ASU: 1.00 Multiplicity: 10 Contiguity score: 1.000 Self-overlap score: 0.154 NXop refinement- correlation before: 0.528, after: 0.577 NXop old: 57.2 179.7 -122.3 -5.5 39.0 64.4 -5.6 10.0 36.4 NXop new: -94.6 179.8 85.4 -3.8 36.5 60.3 -3.8 12.5 40.6 NCS operator: 3 NCS masking: Mask volume as fraction of ASU: 0.95 Multiplicity: 9 Contiguity score: 0.999 Self-overlap score: 0.149 NXop refinement- correlation before: 0.447, after: 0.606 NXop old: -100.7 178.5 79.6-17.7 33.0 93.4-17.9 16.17.4 NXop new: -140.4 179.8 39.7 -9.8 36.7 79.4 -9.9 12.4 21.6 NCS operator: 4 NCS masking: Mask volume as fraction of ASU: 0.89 Multiplicity: 9 Contiguity score: 0.998 Self-overlap score: 0.179 NXop refinement- correlation before: 0.423, after: 0.588 NXop old: 100.4 178.5 -79.3-17.9 16.17.4-17.7 33.0 93.4 NXop new: 144.0 179.8 -36.0-24.0 11.7 20.5-23.7 37.5 80.6 NCS operator statistics: Operator_number Mask_volume/ASU Correlation 11.0010.911 20.9980.912 30.9540.863 40.8880.854 $TABLE :Cycle 1 Electron density histograms: $GRAPHS :Protein:N:1,4,5,6::Solvent:N:1,7,8::Simulation:N:1,3,4: $$ rho_min rho_max Simulatn P_init P_trgt P_mod S_init S_mod $$ $$ -0.317 -0.282 0.000 0.000 0.017 0.008 0.000 0.000 -0.282 -0.247 0.000 0.000 0.026 0.014 0.000 0.000 -0.247 -0.212 0.002 0.002 0.036 0.024 0.000 0.000 -0.212 -0.177 0.007 0.007 0.045 0.039 0.000 0.000 -0.177 -0.143 0.022 0.019 0.057 0.056 0.003 0.000 -0.143 -0.108 0.050 0.048 0.064 0.076 0.020 0.000 -0.108 -0.073 0.093 0.094 0.071 0.081 0.069 0.000 -0.073 -0.038 0.142 0.147 0.070 0.090 0.156 0.000 -0.038 -0.003 0.172 0.175 0.072 0.091 0.234 0.000 -0.003 0.032 0.172 0.173 0.068 0.085 0.237 1.000 0.032 0.067 0.141 0.141 0.063 0.075 0.167 0.000 0.067 0.101 0.099 0.094 0.057 0.071 0.080 0.000 0.101 0.136 0.056 0.053 0.053 0.063 0.026 0.000 0.136 0.171 0.029 0.026 0.049 0.053 0.006 0.000 0.171 0.206 0.011 0.012 0.044 0.048 0.001 0.000 0.206 0.241 0.004 0.005 0.038 0.038 0.000 0.000 0.241 0.276 0.001 0.002 0.033 0.033 0.000 0.000 0.276 0.311 0.000 0.001 0.030 0.025 0.000 0.000 0.311 0.345 0.000 0.000 0.025 0.016 0.000 0.000 0.345 0.380 0.000 0.000 0.021 0.014 0.000 0.000 $$ Gamma 0.24162 Log likelihood: 2.920853e+04 Log likelihood (free): 0.00e+00 $TABLE :Cycle 1 SigmaA statistics: $GRAPHS :SigmaA statistics:N:1,2,3: $$ 1/resol^2 sigmaA(s) sigmaA(w) $$ $$ 0.012 0.682 0.675 0.025 0.629 0.635 0.035 0.659 0.664 0.043 0.666 0.670 0.051 0.619 0.638 0.059 0.515 0.593 0.066 0.452 0.656 $$ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to
