Coot

[…] available to researchers upon request to the corresponding authors., initial model of the chimeric reporter was built using the i-tasser server [63]. manual modeling operations were performed in coot [64] and molecular graphics were generated in pymol [65] [available at: http://www.pymol.org]., the primers were synthesized and page purified by idt dna. fugene 6 transfection reagent […]

[…] with xds64. the crystal structure was determined by molecular replacement using the 14-3-3 epsilon structure (pdb: 2br9) as search model. manual model building and refinement were done with coot, ccp4 software suite, and phenix65–67. the final statistics of the refined models are shown in supplementary table 3., proteins were resolved on 4-12% gradient sds-page gels (nupage bis-tris […]

[…] as the search model. the program molrep was used for both molecular replacement steps. well-defined electron density was observed for residues ala2 to asp7 of aβ1-11, which were manually built with coot59. no electron density was observed outside of the binding groove. aβ1-11 residues asp1, ser8 to glu11 could therefore not be built. structure refinement was performed using refmac560. the final […]

[…] tmds and nbds, and in nbd1, that were not seen in our map. these regions were removed from the homology models before proceeding with refinement. the tm helices were then manually adjusted in coot, as a substantial adjustment was needed to move them into density. the domains were then refined in the same steps as outlined for kir6.2, except that before the final manual adjustments in coot […]

[…] the ng loop of srp interacting with the ribosome was manually adjusted using the programme o6364. the kinked region of the srp rna and the signal sequence extension were manually modelled using coot65. homology models for the e. coli secy, sece and secg were generated using phyre2 (ref. 66) based on the x-ray structure of the isolated secyeg from t. thermophilus (pdb: 5ch4). the resulting […]