Raster3D

[…] plants and shaep were normalized to fit into the scale from 1 to 0 and then combined for a consensus score., figures , 4, 5 were prepared using bodil (lehtonen et al., ), molscript2.1.2 (kraulis, ), raster3d3.0.2 (merritt and murphy, ), and vmd1.9.2 (humphrey et al., ). the area under curve (auc) values (tables , ), the early enrichment values (tables , ) were calculated with rocker0.1.4 (lätti […]

[…] al., ). the negative images of the mao-b and mao-a binding cavities shown in figure and c were outlined using panther (niinivehmas et al., , ) and visualized with bodil, molscript (kraulis, ), and raster3d (merritt and murphy, )., all of the 52 derivatives were docked, synthetized and tested experimentally. those 24 compounds that provided ic50 values below 10 μm were tested more thoroughly […]

[…] refinement, as implemented in sculptor []., saxs data were plotted using grace (http://plasma-gate.weizmann.ac.il/grace). ribbon representations were generated with povscript+ [] and raster3d [], applying secondary structure assignments provided by dssp []., an anti-disc1 camelid vhh phage library was generated using mrna obtained from a llama that had been immunized […]

[…] of compounds were created using libcheck (). model building and refinement were made using coot () and refmac () programs, respectively. the graphics were generated using molscript (), bobscript (), raster3d () and pymol (, ) programs. coordinates and structure factors have been deposited to the rcsb protein data bank (pdb). pdb access codes are listed in ., notes. , sodium malonate solution […]

[…] residues in the outliers with a molprobity score of 1.49. the surface area between the macb monomers was calculated using qt-pisa (ccp4 suite). figures were prepared using molscript rendered with raster3d, chimera and pymol., the expression vector pbad24 containing maca-macb-tolc genes of a. baumannii, deletion mutants, or e172q mutant of macb (supplementary table ), were transformed into e. […]

[…] discussed elsewhere (). all simulations were conducted using the amber 14 program suite ()., the analyses were performed with the cpptraj program (). vmd and pymol were used for visualization while raster3d was used to produce the molecular images (,). for the hydration analyses, we first examined the hydration pattern of the individual protein and rna atoms by identifying the h-bonds […]