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<p>Hello<br>
I am new to cryo-em map reconstruction and want to ask for advice about improving the resolution of the final model. Please see below the steps that I applied.<br>
I think my model current resolution is limited by my ability to perform proper refinement.
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<p>- Is there a way to improve the refinement and to check if this best possible final resolution obtained by the experimental data?
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<p>- At such resolution, is it worth performing molecular replacement since there is a pdb file already available from x-ray?
<br>
Thank you very much for your help. <br>
<br>
I am using Relion 3.0 to performing Bayesian polishing, 3d auto-refine and generating mask on 83,000 particles, the final resolution came to be 4.27 A<br>
mask paramters:<br>
lowpass filter map 15 A<br>
Initial binarisation threshold: 0.003 <br>
extend binary map this many pixels:0<br>
add a soft-edge of this many pixels: 6<br>
<br>
== Masking input maps ...<br>
+ randomize phases beyond: 8.28125 Angstroms<br>
== Dividing map by the MTF of the detector ...<br>
+ mtf STAR-file: mtf2_k2_300kV.star<br>
== Applying sqrt(2*FSC/(FSC+1)) weighting (as in Rosenthal & Henderson, 2003) ...<br>
== Fitting straight line through Guinier plot to find B-factor ...<br>
+ fit from resolution: 10<br>
+ fit until resolution: 0<br>
+ slope of fit: -43.0451<br>
+ intercept of fit: -12.7354<br>
+ correlation of fit: 0.908274<br>
+ apply b-factor of: -172.18<br>
== Low-pass filtering final map ... <br>
+ filter frequency: 4.27419<br>
== Writing output files ...<br>
+ Processed map: PostProcess/job064/postprocess.mrc<br>
+ Processed masked map: PostProcess/job064/postprocess_masked.mrc<br>
+ Metadata file: PostProcess/job064/postprocess.star<br>
+ FINAL RESOLUTION: 4.27419<br>
<br>
<br>
<strong style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">I made another 3D classification on the shiny particles and selected one 3D class of 44,000 particles of the highest resolution performed 3d auto-refine, applied same mask and did post-processing
my final resolution became 4.42 A</span></strong> <br>
<br>
+ input mask: MaskCreate/job057/mask.mrc<br>
== Masking input maps ...<br>
+ randomize phases beyond: 8.0303 Angstroms<br>
== Dividing map by the MTF of the detector ...<br>
+ mtf STAR-file: mtf2_k2_300kV.star<br>
== Applying sqrt(2*FSC/(FSC+1)) weighting (as in Rosenthal & Henderson, 2003) ...<br>
== Fitting straight line through Guinier plot to find B-factor ...<br>
+ fit from resolution: 10<br>
+ fit until resolution: 0<br>
+ slope of fit: -49.6022<br>
+ intercept of fit: -12.9622<br>
+ correlation of fit: 0.970846<br>
+ apply b-factor of: -198.409<br>
== Low-pass filtering final map ... <br>
+ filter frequency: 4.41667<br>
== Writing output files ...<br>
+ Processed map: PostProcess/job078/postprocess.mrc<br>
+ Processed masked map: PostProcess/job078/postprocess_masked.mrc<br>
+ Metadata file: PostProcess/job078/postprocess.star<br>
+ FINAL RESOLUTION: 4.41667</p>
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