Dear Almudena,
We actually have a tutorial that goes through the process of defining a solution step by step: http://www.phaser.cimr.cam.ac.uk/index.php/MR_using_keyword_input.
The .sol file is a small text file that just contains the description of how a defined ensemble should be rotated and translated. If you look at that file, you’ll see that it doesn’t contain the ENSEMBLE definitions, so those still have to be provided in the script that refers to the .sol file.
Best wishes,
Randy Read
-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills Road E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
On 3 Jun 2014, at 09:55, Almudena Ponce Salvatierra <[log in to unmask]> wrote:
> Dear all,
>
> thank you for your suggestions, I finally fix the problem as follows. I'll write a summary here for future reference.
>
> 1) Phaser run 1#
>
> - I provide different ensembles
> - I get a solution in which some of them have been placed
>
> 2) Phaser run 2# ERROR
>
> - I provide the ensembles that were not placed in the previous run and REMOVE THE ONES THAT HAD BEEN PLACED
> - I provide the .sol file
> - The program gives the error I sent yesterday
>
> 3) Phaser run 3# it works again
>
> Since you said what happened was that Phaser was not finding something and the .sol file contained information about the ensembles that I removed...
>
> - I provided again all the ensembles I gave in run 1#
> - I provide de .sol file (I understand it will fix the solution of the ensembles from run 1#)
> - It runs
>
> So, this was my fix :-) I hear many times the sentence "fix a solution", but then whenever I asked someone (before yesterday), each person refers to it in an ambiguous way! some say you need to provide phaser with the pdb from the solution you want to fix, some say that you need to provide the .sol file from what you want to fix and then provide only one new ensemble at the time... maybe it would be useful to have some script/example online of the command line itself, so that one knows what to input exactly. Maybe each one's way of explaining the same thing can lead to misunderstandings at the end.
>
> Best wishes,
>
> Have a nice day.
>
> Almudena
>
>
> ---------- Forwarded message ----------
> From: Almudena Ponce Salvatierra <[log in to unmask]>
> Date: 2014-06-03 9:49 GMT+02:00
> Subject: Re: [ccp4bb] phaser issue MR
> To: Airlie McCoy <[log in to unmask]>
>
>
> Dear Airlie,
>
> don't worry, actually it was you who gave me the clue when you told me what the error was standing for. I will try to be a clear as possible:
>
> 1) Phaser run 1#
>
> - I provide different ensembles
> - I get a solution in which some of them have been placed
>
> 2) Phaser run 2# ERROR
>
> - I provide the ensembles that were not placed in the previous run and REMOVE THE ONES THAT HAD BEEN PLACED
> - I provide the .sol file
> - The program gives the error I sent yesterday
>
> 3) Phaser run 3# it works again
>
> Since you said what happened was that Phaser was not finding something and the .sol file contained information about the ensembles that I removed...
>
> - I provided again all the ensembles I gave in run 1#
> - I provide de .sol file (I understand it will fix the solution of the ensembles from run 1#)
> - It runs
>
> So, this was my fix :-) I hear many times the sentence "fix a solution", but then whenever I asked someone (before yesterday), each person refers to it in an ambiguous way! some say you need to provide phaser with the pdb from the solution you want to fix, some say that you need to provide the .sol file from what you want to fix and then provide only one new ensemble at the time... maybe it would be useful to have some script/example online of the command line itself, so that one knows what to input exactly. Maybe each one's way of explaining the same thing can lead to misunderstandings at the end.
>
> I have another question, if you don't mind. How good does the TFZ score get in one of this "iterative Molecular replacement routines"? I am now above 5 (5.4) which I know is "unlikely" but I need to take into account that I start with fragments that maybe are not exactly as they are in the structure (I mean in reality) and also that the model is incomplete, meaning that even though I have now most of it places there are still some regions that are not connected, some others with empty electron density... What would you recommend in this case?
>
> I also have the following warinings:
>
> - Best model and data are insufficient to reach half expected LLG target: placement of one/first ensemble will be very difficult.
>
> - Search request requires more scattering than defined in composition. Composition increased to accomodate search components.
>
> Thank you very much for your time and consideration.
>
> Best wishes,
>
> Almudena.
>
>
>
> 2014-06-02 22:33 GMT+02:00 Airlie McCoy <[log in to unmask]>:
>
> 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
>
>
>
>
>
>
>
>
> --
> 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
>
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