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The model was manually completed using COOT and was refined with PHENIX.
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Primary amino acid sequences alignments for AtpD were completed using clustalW and manually curated based on tertiary structure predictions (see Methods below).
For cases in which a relatively manageable number of site-level datasets are integrated, merging can often be done manually and well informed quality control and assurance can be completed using expert knowledge of individual datasets.
The annotation was completed using the program DOGMA [ 53] and modified manually to avoid overlap of tRNA and protein-coding genes.
Annotation was completed using the genome annotation system GenDB [ 17], and manually optimized.
Models were manually completed and adjusted with COOT (Emsley et al., 2010) and the structures were refined using REFMAC5 (Murshudov et al., 2011) and phenix.refine (Afonine et al., 2012).
interRAI PURS may be used clinically both as an automated output from a computer-entered MDS assessment, as well as from a manually completed bedside form.
Finally, additional refinements in the XZ (coronal) plane (Figure 3) were again manually completed.
Questionnaires were manually completed by the interviewers.
The mouse reconstruction was then manually completed and validated.
The search was completed manually using references from identified studies and reviews [ 17], and contact was made with experts in the field.
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