- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Thomas Cheatham III <tec3.utah.edu>

Date: Wed, 27 Apr 2011 10:14:00 -0600 (Mountain Daylight Time)

*> > On Wed, Apr 20, 2011 at 1:06 PM, Kamali Sripathi <ksripath.umich.edu>
*

*> > wrote:
*

*> > you no longer have a function (i.e., -181 degrees and 179 degrees are the
*

*> > same angle, yet both
*

*> > are within your range!)
*

*> >
*

*> > This is actually what I often see, so sometimes it's difficult for me to
*

*> tell which angle (i.e, -181º or 179º) is the real dihedral angle.
*

Both are the "real" dihedral angle and it is always a question of

interpretation. Moreover, if the torsion values actually populate values

across the whole range from 0->360, a straight coordinate average will not

work and there is no way to range shift to avoid discontinuities in a

non-circular/non-radial plot.

In ptraj, you can add in at the end of the file (when calculating

dihedrals, distances, etc):

analyze statistics all

...and this will show distributions and averages. Here I calculated a DNA

gamma angle (noting the extra "tag gamma" which provides extra summary

information about these angles).

dihedral g0 out dihedrals/g0.dat :1.O5' :1.C5' :1.C4' :1.C3' type gamma

The results are:

STATISTICS g0

AVERAGE: 53.0966 (47.7803 stddev)

INITIAL: 42.9687

FINAL: 60.2678

g+ a+ t a- g- c

-------------------------------------------------------

%occupied | 89.7 | 0.4 | 5.3 | 0.1 | 4.5 | 0.0 |

average | 59.8 | 104.0 | 177.1 | -111.0 | -63.7 | -20.2 |

stddev | 10.2 | 19.4 | 10.6 | 23.0 | 10.2 | 8.5 |

-------------------------------------------------------

GAMMA canonical minor minor

O5'-C5'-C4'-C3', SNB range is 20-80 (g+)

To get the correct average when the angle populates a wide range, you need

to use circular averaging (and this is what ptraj does with the analyze

routines), i.e.

arctan2( summation( sin(a) ) / n + summation( cos(a) ) / n )

(search "circular averaging" in google for more information).

As mentioned previously on the list, I think by Simmerling, for "plotting"

we typically just show the dots/points (not the full line) since then you

do not see these large jumps in the values when changing from -179 to

+181.

In the analyze.c code is special recognition for certain angles that have

defined ranges so you know what the offsets should be (i.e. if you know

the angle tends to populate +60 you can range shift as you are doing the

averaging / progression to avoid the discontinuities), however in general

there is not a great solution if the angle actually populates fully

through 0-360 except not to show the line or to use radial plots.

--tec3

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Apr 27 2011 - 09:30:04 PDT

Date: Wed, 27 Apr 2011 10:14:00 -0600 (Mountain Daylight Time)

Both are the "real" dihedral angle and it is always a question of

interpretation. Moreover, if the torsion values actually populate values

across the whole range from 0->360, a straight coordinate average will not

work and there is no way to range shift to avoid discontinuities in a

non-circular/non-radial plot.

In ptraj, you can add in at the end of the file (when calculating

dihedrals, distances, etc):

analyze statistics all

...and this will show distributions and averages. Here I calculated a DNA

gamma angle (noting the extra "tag gamma" which provides extra summary

information about these angles).

dihedral g0 out dihedrals/g0.dat :1.O5' :1.C5' :1.C4' :1.C3' type gamma

The results are:

STATISTICS g0

AVERAGE: 53.0966 (47.7803 stddev)

INITIAL: 42.9687

FINAL: 60.2678

g+ a+ t a- g- c

-------------------------------------------------------

%occupied | 89.7 | 0.4 | 5.3 | 0.1 | 4.5 | 0.0 |

average | 59.8 | 104.0 | 177.1 | -111.0 | -63.7 | -20.2 |

stddev | 10.2 | 19.4 | 10.6 | 23.0 | 10.2 | 8.5 |

-------------------------------------------------------

GAMMA canonical minor minor

O5'-C5'-C4'-C3', SNB range is 20-80 (g+)

To get the correct average when the angle populates a wide range, you need

to use circular averaging (and this is what ptraj does with the analyze

routines), i.e.

arctan2( summation( sin(a) ) / n + summation( cos(a) ) / n )

(search "circular averaging" in google for more information).

As mentioned previously on the list, I think by Simmerling, for "plotting"

we typically just show the dots/points (not the full line) since then you

do not see these large jumps in the values when changing from -179 to

+181.

In the analyze.c code is special recognition for certain angles that have

defined ranges so you know what the offsets should be (i.e. if you know

the angle tends to populate +60 you can range shift as you are doing the

averaging / progression to avoid the discontinuities), however in general

there is not a great solution if the angle actually populates fully

through 0-360 except not to show the line or to use radial plots.

--tec3

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Apr 27 2011 - 09:30:04 PDT

Custom Search