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To facilitate system maintenance and reconfiguration, all the correctly configured options can be saved to a text file, which can be manually modified as required.
The alignments were then manually modified as required and the modelling and validation process repeated.
Mispredicted genes, if found, were manually modified as follows.
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All identified peptide variants, modified as well as non-modified, were sequenced in at least two separate LC/MS/MS runs of histones extracted from the same person and all spectra were manually verified.
Authors' response: modified as suggested.
For calculation of difference maps scripts from the CCP4 program suite package were manually modified and used at each step as indicated in brackets.
Starting from the BLAST alignment between P. brasiliensis TRR1 and KRE2 proteins with the PDB templates as found above, we manually modified them in order to preserve the secondary structures and the correspondence between cysteine residues (Additional file 6a and 6b).
However, this study included solid 15- to 500-mm nodules only, and if readers manually modified the volume in the prospective lung cancer screening study, the nodules were excluded as well.
If an error is detected, the program or the model is manually modified and verified again.
The alignments were manually modified to correct defects from the automatic alignment method of ClustalW.
Figure 12(g) is a manually modified edge from the edge map of Figure 12(f).
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com