![]() The B-factor field is then filled with the Van der Waals radius Is that the input file is a run input file. Program (Poisson-Boltzmann solver) can be made. Maximum value found, effectively making a legend for viewing. legend will produceĪ row of CA atoms with B-factors ranging from the minimum to the Obviously, any type of numeric data canīe added instead of B-factors. Unless the number of B-factors is larger than the number of the residues or unless the The B-factors will be attached per residue B-factors are readįrom a file with with following format: first line states number ofĮntries in the file, next lines state an indexįollowed by a B-factor. pdb files, B-factors can beĪdded with the -bf option. It is important that the box vectors at the bottom of your input fileĪre correct when the periodicity is to be removed. Periodicity can be removed in a crude manner. Groups are selected after all operations have been applied. A special feature of the scaling option is that when theįactor -1 is given in one dimension, one obtains a mirror image, Note that this may be inaccurate in case a. Boxes and coordinates can be scaled to give a certain density (option Scaling is applied before any of the other operations are This may allow you to decrease the box volume,īut beware that molecules can rotate significantly in a nanosecond. princ aligns the principal axes of the system along theĬoordinate axes, with the longest axis aligned with the x-axis. rotate rotates the coordinates and velocities. Option -angles is only meaningful with option -box andĪ triclinic box and cannot be used with option -d.Ĭan be selected for calculating the size and the geometric center, To the diameter of the system (largest distance between atoms) plus twice With -d and cubic,ĭodecahedron or octahedron boxes, the dimensions are set With -d and a triclinic box the size of the system in the x-,Īnd z-directions is used. One value for a cubic, rhombic dodecahedral, or truncated octahedral box. Relative to a cubic box with some periodic image distance, the volume of aĭodecahedron with this same periodic distance is 0.71 times that of the cube,Īnd that of a truncated octahedron is 0.77 times. Shortest distance between two opposite hexagons. The length of the three box vectors of the truncated octahedron is the The last two are special cases of a triclinic box. Triclinic box, cubic is a rectangular box with all sides equalĭodecahedron represents a rhombic dodecahedron and Option -bt determines the box type: triclinic is a Of the system from the default of (x/2, y/2, z/2) implied by -c The -center option can be used to shift the geometric center Will center the system in the box, unless -noc is used. The box can be modified with options -box, -d and Gmx editconf converts generic structure format to. ![]()
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