Usage:
play operation arguments

The play command performs complex motions for creating animations. The operation can be:

• radial - move multiscale chain surfaces radially.
• wave - move multiscale chain surfaces from an initial to final state.
• wiggle - wiggle branches of a molecule.
• zipper - move residues from an initial to final state sequentially.

Example animation

Operation keywords and their sub-keywords described below can be truncated to unique strings, and their case does not matter. Synonyms for true: True, 1. Synonyms for false: False, 0. A vertical bar "|" designates mutually exclusive options, and default settings are indicated with bold.

Move multiscale chain surfaces radially from the center of all surfaces. The center of each chain surface moves radially from the common center for a total expansion by the specified factor over N frames. Examples of surface specifiers: #0, #1:1-30, #2:.A,.C, #3:.A-H, #4:31-60.S-V This command was developed to peel off outer layers of proteins from virus capsid models.

Example animation

Moves multiscale chain pieces from an initial position to a final position. The motion begins at the first chain and propagates out moving additional chains based on their distance from already moved chains. The pairings of chains between initial and final states can computed to minimize overall motion. The pairChains option specifies a correspondence between initial and final chain identifiers. For example "pairChains A=S,B=T,C=U" identifies chains A,B,C in the intial state as matching chains S,T,U in the final state. If the option is not given then the same chain identifiers in the initial and final states are matched. The groupChains option allows moving 2 or more chains as a single rigid object, for example "groupChains A+D,B+E,C+F" makes chains A and D move as a single unit, likewise B and E, also C and F. The equivalentChains option lists chains (or groups) in the initial state are equivalent to each other for purposes of pairing initial state and final state chains. For example, "equivalentChains A=B=C" says that chains A, B, and C are all interchangeable when pairing with final state chains. If chains are grouped then "equivalentChains A+D=B+E=C+F" can express the groups that are equivalent for pairing. The pairingMethod option specifies an algorithm for how chains of the initial state are paired with those of the final state. The default value "match" matches the chain instance numbers, ie chains 1-60 match 1-60 in order. The "push" method matches an initial chain to the nearest final state chain position that is not yet paired. The "pull" method matches each final state chain to the nearest initial state chain that has not been paired. The "pushpull" method does first push pairing then pull pairing in each layer of chains where each layer consists of chains within distanceStep of the previous layer. The push and pull methods can make the last moved chains fly a long distance, while the pushpull method avoids this problem. Paired chains must have identical sets of atoms because the motion of the intial state to the final state is computed by a minimum RMSD match between corresponding atom positions. This command was developed for showing the conformational rearrangement of dengue virus capsid proteins during virus maturation.

Example animation

Wiggle branches of a molecule back and forth where a branch is a contiguous range of residues. Each branch is rotated about an axis defined by two end atoms. One end atoms comes from a residue at each end of the contiguous sequence defining the branch and has a bond to the next residue outside the range of the branch. The rotation angle from the original position varies sinusoidally with time. The speed of motion of a branch is inversely proportional to the number of atoms in the branch. The atoms argument is the set in which the branches are defined while the branches argument is a comma-separated list of residue ranges, each range defining defining a branch, for example, "branches 35-85,53-65,121-290". Then angle option specifies the maximum rotation in degrees (default 10). The speed option (default 25) controls the speed of rotation, one wiggle oscillation taking a number of frames equal to the number atoms in the branch divided by the speed. The cycle time for a branch is adjust to the nearest value that makes a half-integral number of cycles complete in the specified frames, so that after the wiggle ends all atoms are in their original positions. The frames argument is the number of frames the motion is carried out over. This command was developed to illustrate flexibility of the 9000 nucleotide HIV RNA genome.

Example animation

This command linearly intepolates the atom positions from an initial state to a final state starting at one end of a chain of residues and progress over time to the other end. It moves the initial state to the final state like the action of closing a zipper. Each residue list must belong to one molecule and the lists must have the same number of residues. The residues will be paired in the order they are specified. The residue numbers need not match. Residues in list one are moved. The atoms of a residue in the first list are paired with the atoms of the corresponding residue in the second list by matching atom names. Unpaired atoms are not moved. If f represents the fraction for interpolating residue atoms with f = 0 being the initial state and f = 1 being the final state then f varies with residue number as a piecewise linear function, f = 1 for initial residues, then a linear ramp down to 0, then f = 0 for final residues in the chain. The linear ramp is progressively moved from start to end of the chain, animating the change. The width of the linear ramp is proportional to the distance between residue centers at the start of the ramp in the two states, that distance being divided by the spacing parameter (default 3) to obtain the width in number of residues. Each frame the ramp advances by a number of residues equal to the step parameter (default 1). The step can be non-integer, for example 0.1 for a slower motion. Negative step values make the motion begin at the last residue and proceed to the first. This was originally used in an HIV RNA movie to show RNA being synthesized from a DNA template.