Hi Almundena, Apologies, I had not had a chance to look at it... what was your fix? Airlie
On Jun 2 2014, Almudena Ponce Salvatierra wrote:
Dear Airlie,
I already solved the problem.
Thank you very much anyway.
Best wishes,
Almudena
2014-06-02 15:43 GMT+02:00 Almudena Ponce Salvatierra <[log in to unmask]>
:
Sorry, Airlie, the input is this one,
ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT
$TEXT:Script: $$ Baubles Markup $$
#---PHASER COMMAND SCRIPT GENERATED BY CCP4I---
TITLE start
MODE MR_AUTO
ROOT "/data/almudena/ccp4/iterativeMR/may_attempt/epmrsol/epmr_24"
#---DEFINE DATA---
HKLIN "/data/almudena/ccp4/iterativeMR/epmr/forccp4_itMR.mtz"
LABIN F=FP SIGF=SIGFP
SGALTERNATIVE SELECT HAND
#---DEFINE ENSEMBLES---
ENSEMBLE loop &
PDB "/data/almudena/ccp4/iterativeMR/epmr/epmr_start_6bp/4ntloop-coot-0.pdb" &
IDENT 99.0
ENSEMBLE 6bp &
PDB &
"/data/almudena/ccp4/iterativeMR/epmr/epmr_start_6bp/Ideal-A-5bpform-RNA-coot-4.pdb &
" IDENT 99.0
ENSEMBLE 5bp &
PDB &
"/data/almudena/ccp4/iterativeMR/epmr/epmr_start_6bp/Ideal-A-6bpform-RNA-coot-0.pdb &
" IDENT 99.0
#---DEFINE COMPOSITION---
COMPOSITION BY ASU
COMPOSITION NUCLEIC MW 2000 NUMBER 1
COMPOSITION NUCLEIC MW 3500 NUMBER 1
COMPOSITION NUCLEIC MW 3000 NUMBER 1
#---SEARCH PARAMETERS---
SEARCH ENSEMBLE loop NUMBER 1
SEARCH ENSEMBLE 6bp NUMBER 1
SEARCH ENSEMBLE 5bp NUMBER 1
#@ "/data/almudena/ccp4/iterativeMR/may_attempt/epmrsol/epmr_23.sol"
Thank you very much for your help.
Best,
Almudena
2014-06-02 15:40 GMT+02:00 Almudena Ponce Salvatierra <
[log in to unmask]>:
Dear Airlie,
this is my input:
$TEXT:Script: $$ Baubles Markup $$
#---PHASER COMMAND SCRIPT GENERATED BY CCP4I---
TITLE start
MODE MR_AUTO
ROOT "/data/almudena/ccp4/iterativeMR/may_attempt/epmrsol/epmr_25"
#---DEFINE DATA---
HKLIN "/data/almudena/ccp4/iterativeMR/epmr/forccp4_itMR.mtz"
LABIN F=FP SIGF=SIGFP
SGALTERNATIVE SELECT HAND
#---DEFINE ENSEMBLES---
ENSEMBLE loop &
PDB "/data/almudena/ccp4/iterativeMR/epmr/epmr_start_6bp/4ntloop-coot-0.pdb" &
IDENT 99.0
ENSEMBLE 6bp &
PDB &
"/data/almudena/ccp4/iterativeMR/epmr/epmr_start_6bp/Ideal-A-5bpform-RNA-coot-4.pdb &
" IDENT 99.0
ENSEMBLE 5bp &
PDB &
"/data/almudena/ccp4/iterativeMR/epmr/epmr_start_6bp/Ideal-A-6bpform-RNA-coot-0.pdb &
" IDENT 99.0
#---DEFINE COMPOSITION---
COMPOSITION BY ASU
COMPOSITION NUCLEIC MW 2000 NUMBER 1
COMPOSITION NUCLEIC MW 3500 NUMBER 1
COMPOSITION NUCLEIC MW 3000 NUMBER 1
COMPOSITION NUCLEIC MW 6500 NUMBER 1
#---SEARCH PARAMETERS---
SEARCH ENSEMBLE loop NUMBER 1
SEARCH ENSEMBLE 6bp NUMBER 1
SEARCH ENSEMBLE 5bp NUMBER 1
#@ "/data/almudena/ccp4/iterativeMR/may_attempt/epmrsol/epmr_23.sol"
And this is the .sol I got from the previous run:
start SOLU SET RFZ=2.2 TFZ=5.4 PAK=0 LLG=50 RFZ=2.0 TFZ=5.1 PAK=1 LLG=31 SOLU SPAC P 43 21 2 SOLU 6DIM ENSE 4bp EULER 16.341 63.567 30.174 FRAC 0.22185 0.44226 0.03952 BFAC -7.49187 SOLU 6DIM ENSE 7bp EULER 241.601 118.980 153.727 FRAC -0.01556 1.86158 -2.79161 BFAC 16.21737 SOLU ENSEMBLE 4bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU ENSEMBLE 7bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU SET RFZ=2.3 TFZ=5.1 PAK=0 LLG=45 RFZ=2.2 TFZ=4.4 PAK=1 LLG=29 SOLU SPAC P 43 21 2 SOLU 6DIM ENSE 4bp EULER 66.372 61.960 58.237 FRAC 0.45058 0.63587 0.81100 BFAC -5.80353 SOLU 6DIM ENSE 7bp EULER 19.844 109.156 175.316 FRAC -0.32601 0.71314 -2.71641 BFAC 14.21615 SOLU ENSEMBLE 4bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU ENSEMBLE 7bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU SET RFZ=2.0 TFZ=4.9 PAK=0 LLG=44 RFZ=2.1 TFZ=5.2 PAK=1 LLG=28 SOLU SPAC P 43 21 2 SOLU 6DIM ENSE 4bp EULER 262.125 56.041 91.432 FRAC -1.55717 0.91455 0.61038 BFAC -6.80573 SOLU 6DIM ENSE 7bp EULER 327.770 65.111 22.515 FRAC -0.83412 0.54719 1.82357 BFAC 16.22672 SOLU ENSEMBLE 4bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU ENSEMBLE 7bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU SET RFZ=2.3 TFZ=4.0 PAK=0 LLG=43 RFZ=2.0 TFZ=4.8 PAK=2 LLG=28 SOLU SPAC P 43 21 2 SOLU 6DIM ENSE 4bp EULER 250.594 60.709 57.296 FRAC -0.67496 1.19211 1.45604 BFAC -6.52229 SOLU 6DIM ENSE 7bp EULER 243.872 70.588 9.146 FRAC 0.63406 0.31060 2.04320 BFAC 15.75047 SOLU ENSEMBLE 4bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU ENSEMBLE 7bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU SET RFZ=2.2 TFZ=5.4 PAK=0 LLG=50 RFZ=1.7 TFZ=4.3 PAK=2 LLG=27 SOLU SPAC P 43 21 2 SOLU 6DIM ENSE 4bp EULER 16.341 63.567 30.174 FRAC 0.22185 0.44226 0.03952 BFAC -7.49187 SOLU 6DIM ENSE 7bp EULER 67.735 53.472 90.204 FRAC 2.14373 -0.56441 -1.44519 BFAC 16.50875 SOLU ENSEMBLE 4bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU ENSEMBLE 7bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU SET RFZ=2.0 TFZ=4.9 PAK=0 LLG=44 RFZ=2.2 TFZ=5.2 PAK=2 LLG=25 SOLU SPAC P 43 21 2 SOLU 6DIM ENSE 4bp EULER 262.125 56.041 91.432 FRAC -1.55717 0.91455 0.61038 BFAC -6.80573 SOLU 6DIM ENSE 7bp EULER 20.896 119.163 190.718 FRAC -1.01891 -0.61652 -1.58491 BFAC 15.81504 SOLU ENSEMBLE 4bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU ENSEMBLE 7bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU SET RFZ=2.0 TFZ=4.9 PAK=0 LLG=44 RFZ=2.1 TFZ=4.8 PAK=0 LLG=24 SOLU SPAC P 43 21 2 SOLU 6DIM ENSE 4bp EULER 262.125 56.041 91.432 FRAC -1.55717 0.91455 0.61038 BFAC -6.80573 SOLU 6DIM ENSE 7bp EULER 242.616 115.771 183.299 FRAC -0.60830 1.00840 -2.03348 BFAC 15.23114 SOLU ENSEMBLE 4bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU ENSEMBLE 7bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU SET RFZ=2.3 TFZ=4.3 PAK=0 LLG=43 RFZ=2.0 TFZ=4.7 PAK=3 LLG=22 SOLU SPAC P 43 21 2 SOLU 6DIM ENSE 4bp EULER 69.059 60.084 57.214 FRAC 0.46363 0.62068 0.59030 BFAC -6.07784 SOLU 6DIM ENSE 7bp EULER 149.705 110.295 175.438 FRAC 0.99548 2.34497 -2.92000 BFAC 15.05712 SOLU ENSEMBLE 4bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU ENSEMBLE 7bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU SET RFZ=2.3 TFZ=4.3 PAK=0 LLG=43 RFZ=2.0 TFZ=4.7 PAK=1 LLG=22 SOLU SPAC P 43 21 2 SOLU 6DIM ENSE 4bp EULER 69.059 60.084 57.214 FRAC 0.46363 0.62068 0.59030 BFAC -6.07784 SOLU 6DIM ENSE 7bp EULER 213.189 68.109 354.911 FRAC 0.91144 1.23250 0.85333 BFAC 15.72042 SOLU ENSEMBLE 4bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU ENSEMBLE 7bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU SET RFZ=2.3 TFZ=4.0 PAK=0 LLG=43 RFZ=2.0 TFZ=4.3 PAK=0 LLG=20 SOLU SPAC P 43 21 2 SOLU 6DIM ENSE 4bp EULER 250.594 60.709 57.296 FRAC -0.67496 1.19211 1.45604 BFAC -6.52229 SOLU 6DIM ENSE 7bp EULER 122.751 66.950 356.569 FRAC -0.46975 -1.02260 1.68062 BFAC 14.84964 SOLU ENSEMBLE 4bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU ENSEMBLE 7bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU SET RFZ=2.3 TFZ=4.0 PAK=0 LLG=43 RFZ=2.0 TFZ=4.9 PAK=0 LLG=18 SOLU SPAC P 43 21 2 SOLU 6DIM ENSE 4bp EULER 250.594 60.709 57.296 FRAC -0.67496 1.19211 1.45604 BFAC -6.52229 SOLU 6DIM ENSE 7bp EULER 211.408 68.304 357.378 FRAC 0.56201 -0.13890 1.77485 BFAC 14.71509 SOLU ENSEMBLE 4bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU ENSEMBLE 7bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU SET RFZ=2.3 TFZ=5.1 PAK=0 LLG=45 RFZ=2.2 TFZ=4.4 PAK=1 LLG=13 SOLU SPAC P 43 21 2 SOLU 6DIM ENSE 4bp EULER 66.372 61.960 58.237 FRAC 0.45058 0.63587 0.81100 BFAC -5.80353 SOLU 6DIM ENSE 7bp EULER 195.245 112.236 173.632 FRAC 0.41506 2.83682 -2.78241 BFAC 14.31749 SOLU ENSEMBLE 4bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37 SOLU ENSEMBLE 7bp VRMS DELTA +0.0000 RMSD 0.37 #VRMS 0.37
Thank you very much in advance. Is, in principle, what I said I did, correct?
Best wishes,
Almudena
2014-06-02 15:34 GMT+02:00 Airlie McCoy <[log in to unmask]>:
Hi Almudena
Can you send me a copy of your input script and the sol file? The error message should be a little less cryptic - it means that phaser is looking for an ensemble that does not exist in memory.
Thanks, Airlie
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany