Difference between revisions of "Mset"
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'''mset''' sets up a relationship between molecular states and movie frames. This makes it possible to control which states are shown in which frame. | '''mset''' sets up a relationship between molecular states and movie frames. This makes it possible to control which states are shown in which frame. | ||
| − | == | + | The related command '''madd''' appends to the end of a movie. It is identical to the '''mset''' command, except for the default value of the '''frame''' argument (0 instead of 1). |
| − | mset specification [ ,frame ] | + | |
| + | == Usage == | ||
| + | |||
| + | mset specification [, frame ] | ||
| + | madd specification [, frame ] | ||
| + | |||
| + | == Arguments == | ||
| + | |||
| + | * '''specification''' = str: state sequence (see below for syntax), or empty string to delete movie {default: } | ||
| + | * '''frame''' = int: start frame, or 0 to append to the end of an existing movie {default: 1 (0 for madd)} | ||
| + | |||
| + | == Specification Syntax == | ||
| + | |||
| + | The state sequence specification consists of numbers, and the operators "x" and "-". Spaces between operators are optional. | ||
| + | |||
| + | Operator semantic: | ||
| + | |||
| + | * ''state'' '''x''' ''count'': Repeat state ''state'' for ''count'' frames | ||
| + | * ''state1'' '''-''' ''state2'': Iterate from ''state1'' to ''state2'', yields ''abs(state1 - state2) + 1'' frames | ||
| + | |||
| + | Formal syntax description: | ||
| + | |||
| + | * ''specification'' ::= ''state'' ['''x''' ''count''] {'''-''' ''specification''} [''specification''] | ||
| + | * ''state'' ::= '''number''' | ||
| + | * ''count'' ::= '''number''' | ||
| + | |||
| + | == Examples == | ||
| − | |||
<source lang="python"> | <source lang="python"> | ||
| − | + | mset 1 # simplest case, one state -> one frame | |
| − | + | mset 1 x10 # ten frames, all corresponding to state 1 | |
| + | mset 1 1 1 1 1 1 1 1 1 1 # identical to previous | ||
| + | mset 1-20 # map a 20 state trajectory to 20 frames | ||
| + | mset 1 2 3 4 5-20 # identical to previous | ||
| − | |||
| − | |||
| − | |||
| − | |||
mset 1 x30 1 -15 15 x30 15 -1 | mset 1 x30 1 -15 15 x30 15 -1 | ||
| − | + | # more realistic example: | |
| − | + | # the first thirty frames are state 1 | |
| − | + | # the next 15 frames pass through states 1-15 | |
| − | + | # the next 30 frames are of state 15 | |
| − | + | # the next 15 frames iterate back to state 1 | |
</source> | </source> | ||
| Line 30: | Line 54: | ||
<source lang="python"> | <source lang="python"> | ||
cmd.mset("1 -%d" % cmd.count_states()) | cmd.mset("1 -%d" % cmd.count_states()) | ||
| − | + | # this will create a one-to-one mapping of states to movie frames. useful for making movies from trajectory files. | |
</source> | </source> | ||
| − | === | + | == PyMOL API == |
| + | |||
| + | <source lang="python"> | ||
| + | cmd.mset(string specification, int frame=1) | ||
| + | cmd.madd(string specification, int frame=0) | ||
| + | </source> | ||
| + | |||
| + | == See Also == | ||
| + | |||
[[mdo]], [[mplay]], [[mclear]] | [[mdo]], [[mplay]], [[mclear]] | ||
[[Category:Commands|Mset]] | [[Category:Commands|Mset]] | ||
[[Category:States|Mset]] | [[Category:States|Mset]] | ||
Latest revision as of 11:27, 28 October 2015
mset sets up a relationship between molecular states and movie frames. This makes it possible to control which states are shown in which frame.
The related command madd appends to the end of a movie. It is identical to the mset command, except for the default value of the frame argument (0 instead of 1).
Usage
mset specification [, frame ] madd specification [, frame ]
Arguments
- specification = str: state sequence (see below for syntax), or empty string to delete movie {default: }
- frame = int: start frame, or 0 to append to the end of an existing movie {default: 1 (0 for madd)}
Specification Syntax
The state sequence specification consists of numbers, and the operators "x" and "-". Spaces between operators are optional.
Operator semantic:
- state x count: Repeat state state for count frames
- state1 - state2: Iterate from state1 to state2, yields abs(state1 - state2) + 1 frames
Formal syntax description:
- specification ::= state [x count] {- specification} [specification]
- state ::= number
- count ::= number
Examples
mset 1 # simplest case, one state -> one frame
mset 1 x10 # ten frames, all corresponding to state 1
mset 1 1 1 1 1 1 1 1 1 1 # identical to previous
mset 1-20 # map a 20 state trajectory to 20 frames
mset 1 2 3 4 5-20 # identical to previous
mset 1 x30 1 -15 15 x30 15 -1
# more realistic example:
# the first thirty frames are state 1
# the next 15 frames pass through states 1-15
# the next 30 frames are of state 15
# the next 15 frames iterate back to state 1
mset 1 x200 -78 -2 -78 -2 -78 x200 79 -156 157 x200 -234 235 x400
# mset 1 x200 makes the first state last for 200 frames
# -78 -2 takes us FROM state 1 to 78, then back to frame 2. I've repeated this for dramatic effect.
# Then we pause at 78 for 200 frames, then go from 79-156 and pause at 157 for 200 frames, etc.
cmd.mset("1 -%d" % cmd.count_states())
# this will create a one-to-one mapping of states to movie frames. useful for making movies from trajectory files.
PyMOL API
cmd.mset(string specification, int frame=1)
cmd.madd(string specification, int frame=0)