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Thanks for reporting this anyway. I agree the script is not so user-friendly and will probably update it. But if you find the rows of the the partiles are in random order, don't worry abouth that. Each particle still points to exactly the correct .mrcs file, it just looks a bit ugly in such a random order. Best wishes, Kai > Sorry, I jumped the gun. I fixed it. > > > Zachary Berndsen, PhD > > The Scripps Research Institute > > Hazen Building (HL 104) > > Ward Lab > > ________________________________ > From: Collaborative Computational Project in Electron cryo-Microscopy > <[log in to unmask]> on behalf of Zack Berndsen <[log in to unmask]> > Sent: Wednesday, November 30, 2016 1:04:58 PM > To: [log in to unmask] > Subject: Re: [ccpem] Relion/2.0 GCTF wrapper errors > > > Hi Kai, > > > star_replaceUVA.com is not working properly for me. It's mixing up > columns. Particles were extracted from the mics_all_gctf.star file and no > processing was performed on the extracted particles. I am attempting to > replace ctf info in the extracted particles.star file with the the local > ctf info. > > > Here is the the original particles.star file with the correct columns: > > > data_ > > > loop_ > > _rlnCoordinateX #1 > > _rlnCoordinateY #2 > > _rlnImageName #3 > > _rlnMicrographName #4 > > _rlnVoltage #5 > > _rlnDefocusU #6 > > _rlnDefocusV #7 > > _rlnDefocusAngle #8 > > _rlnSphericalAberration #9 > > _rlnCtfBfactor #10 > > _rlnCtfScalefactor #11 > > _rlnPhaseShift #12 > > _rlnAmplitudeContrast #13 > > _rlnMagnification #14 > > _rlnDetectorPixelSize #15 > > _rlnCtfFigureOfMerit #16 > > 2199.450878 800.450878 > [log in to unmask] > mc2_5x5_Bft300_ref0/16aug05c_00003sq_00004hl_00002esup-a_movie_DW.mrc > 300.000000 26826.996094 26031.109375 86.949692 2.700000 > 0.000000 1.000000 0.000000 0.100000 38168.000000 5.000000 > 0.132110 > > > > Here is the the particles_localUVA.star file generated by > star_replaceUVA.com: > > > > data_ > > > loop_ > > _rlnCoordinateX #1 > > _rlnCoordinateY #2 > > _rlnImageName #3 > > _rlnMicrographName #4 > > _rlnVoltage #5 > > _rlnDefocusU #6 > > _rlnDefocusV #7 > > _rlnDefocusAngle #8 > > _rlnSphericalAberration #9 > > _rlnCtfBfactor #10 > > _rlnCtfScalefactor #11 > > _rlnPhaseShift #12 > > _rlnAmplitudeContrast #13 > > _rlnMagnification #14 > > _rlnDetectorPixelSize #15 > > _rlnCtfFigureOfMerit #16 > > 3045.048009 1922.652009 > [log in to unmask] > > mc2_5x5_Bft300_ref0/16aug05c_a_00012gr_00112sq_00011hl_00003esup-a_movie_DW.mrc > 300.000000 2.700000 0.000000 1.000000 0.000000 0.100000 > 38168.000000 5.000000 0.187550 > > The columns are clearly incorrect. DU and DV are suppose to follow voltage > but CS does instead. > > Here is one of the ctf_local.star files with the correct columns: > > > > data_ > > > loop_ > > _rlnMicrographName #1 > > _rlnCoordinateX #2 > > _rlnCoordinateY #3 > > _rlnVoltage #4 > > _rlnDefocusU #5 > > _rlnDefocusV #6 > > _rlnDefocusAngle #7 > > _rlnSphericalAberration #8 > > _rlnDetectorPixelSize #9 > > _rlnCtfFigureOfMerit #10 > > _rlnMagnification #11 > > _rlnAmplitudeContrast #12 > > _rlnAutopickFigureOfMerit #13 > > mc2_5x5_Bft300_ref0/16aug05c_00003sq_00010hl_00002esup-a_movie.mrc > 1294.000000 2701.000000 300.000000 24318.199219 23865.933594 > 74.219482 2.700000 14.000000 0.065700 106870.234375 > 0.100000 0.000000 > > > > > I can edit my star_replaceUVA.com script to reference the correct columns > if that is the problem, you'll just have to point me to the correct lines. > > > Thanks, > > > Zachary Berndsen, PhD > > The Scripps Research Institute > > Hazen Building (HL 104) > > Ward Lab > > ________________________________ > From: Zack Berndsen > Sent: Tuesday, November 29, 2016 3:16:58 PM > To: [log in to unmask]; Zack Berndsen > Subject: Re: Relion/2.0 GCTF wrapper errors > > > Kai, > > > I attempted a local ctf run with a set of reentered > coordinate_extract.star files from a previous relion/2.0 processing run > and it seems to have worked properly. I will read up on the _UVA.com > script but it seems straight forward enough. Thanks a lot for the help. > > > Best, > > > Zachary Berndsen, PhD > > The Scripps Research Institute > > Hazen Building (HL 104) > > Ward Lab > > ________________________________ > From: Collaborative Computational Project in Electron cryo-Microscopy > <[log in to unmask]> on behalf of Zack Berndsen <[log in to unmask]> > Sent: Monday, November 28, 2016 1:17:09 PM > To: [log in to unmask] > Subject: [ccpem] Relion/2.0 GCTF wrapper errors > > > Hi, > > > This is a two part question. First, I am encountering a strange error in > the final steps of GCTF execution through relion/2.0. I have run the > wrapper successfully several times without the error and the solution is > not obvious to me. Here is the error: > > > > ... > > * > MotionCor2_5x5_Bft100_ref0/15feb27c_1_00018gr_00004sq_00017hl_00004ed-a.mrc > > ... > > Estimating CTF parameters using Kai Zhang's Gctf ... > > 5.60/5.60 hrs > ............................................................~~(,_,"> > > +++ RELION: command line arguments (with defaults for optional ones > between parantheses) +++ > > ... > > ERROR: Unexpected number of words on Final values line in > CtfFind/mc2_5x5_ref0_rn2/MotionCor2_5x5_Bft100_ref0/15feb27c_1_00003gr_00021sq_00026hl_00004ed-a_gctf.log > > File: /tmp/relion2-beta/src/ctffind_runner.cpp line: 659 > > > Final few lines of the log file in question (I don't see anything > obviously wrong): > > > ************************************** LAST CYCLE > ************************************************************ * > > > Defocus_U Defocus_V Angle CCC > > 21388.87 20984.57 87.63 0.120526 Final Values > > > Resolution limit estimated by EPA: RES_LIMIT 2.827 > > Estimated Bfactor: B_FACTOR 21.37 > > Processing done successfully. > > 4.59 87.75 0.120526 Final Values > > > Resolution limit estimated by EPA: RES_LIMIT 2.827 > > Estimated Bfactor: B_FACTOR 21.37 > > Processing done successfully. > > > > > Has anyone encountered this before? If so do you know what is causing it > and how to fix it? > > > Second, I've noticed in the log files that the XMAG and DStep are not > being passed to the executable properly (correct values were given in the > command). I know the wrapper is suppose to input the microscopy options > from the gui into the command and ignore gctf defaults but the fact that > they appear incorrect in the log file makes me wonder if they are in fact > being used the in calculations. The apix is correct however and I assume > this is the most important option (does it overwrite the others?). Also, > my previous reconstructions where GCTF was used are great and I can't see > any issues with them so I am assuming I should just ignore these > inconsistencies, but it would be nice to know for sure. Are these values > used in the calculations? See section of log file below: > > > > ... > > GCTF , v0.50 2014-11-05 > > All parameters to be used: > > General options: > > --apix 1.310 > > --dstep 14.000 > > --kv 300.00 > > --cs 2.70 > > --ac 0.10 > > ... > > ******************************** CTFFIND3 parameter format for RELION: > ********************************************* > > > NOTE: NOTHING related to CTFFIND3. Just use it for RELION. > > > Input image file name > > CtfFind/mc2_5x5_ref0_rn2/MotionCor2_5x5_Bft100_ref0/15feb27c_1_00003gr_00021sq_00026hl_00004ed-a.mrc > > > Output diagnostic file name > > CtfFind/mc2_5x5_ref0_rn2/MotionCor2_5x5_Bft100_ref0/15feb27c_1_00003gr_00021sq_00026hl_00004ed-a.ctf > > > CS[mm], HT[kV], AmpCnst, XMAG, DStep[um] > > 2.7 300.0 0.10 106870.2 14.000 > > > Thank you! > > > > Zachary Berndsen, PhD > > The Scripps Research Institute > > Hazen Building (HL 104) > > Ward Lab >