Hi, I have a couple of questions: Is there a simple way to determine the angle between any of the three axes, X,Y or Z and the line connecting two selected atoms?. I know you can use the Angles/Torsions tools to determine the angle formed between 3 sets of atoms, but I wonder if you could use that tool, or some other, to report the angle of two atoms with the axes?. Is it possible to draw a box with the axes around a structure as it can be done with a volume ?. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa@aecom.yu.edu -----------------------------------
On Nov 5, 2007, at 12:24 PM, Hernando Sosa wrote:
Hi, I have a couple of questions:
Is there a simple way to determine the angle between any of the three axes, X,Y or Z and the line connecting two selected atoms?. I know you can use the Angles/Torsions tools to determine the angle formed between 3 sets of atoms, but I wonder if you could use that tool, or some other, to report the angle of two atoms with the axes?.
Hi Hernando, Perhaps you could explain in more detail what you want to determine here. AFAIK, there is no unique angle between non-intersecting lines in 3-space.
Is it possible to draw a box with the axes around a structure as it can be done with a volume ?.
There is no command or GUI for it, but in Python pretty much anything is possible. I've appended a Python script that will draw axis- aligned bounding boxes of currently selected molecules (or all molecule models if none are selected). Just open it with File...Open or the "open" command. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
If you think of the line connecting the two atoms as a vector (with no position in space), then it's angle to another vector (e.g. the x-axis (1,0,0)) can be computed from the definition of dot product: u . v = |u| * |v| * cos ( theta) where u . v is the dot product between the vectors u and v, theta is the angle between the vectors u and v, and |u| is the magnitude (length) of u so cos ( theta) = u . v / ( |u| * |v| ) theta = arccos ( u.v / ( |u| * |v| ) ) if the vectors u and v are normalized / have unit length of 1 then you can simplify: theta = arccos ( u.v ) within chimera, in the python interpreter IDLE, you first need to get the coordinates of the two atoms, for example, to get the vector from the alpha carbon in residue 32 to the alpha carbon in residue 33: at1 = chimera.selection.OSLSelection(":32.A@CA").atoms()[0] at2 = chimera.selection.OSLSelection(":33.A@CA").atoms()[0] v = at2.coord() - at1.coord() v.normalize() import numpy theta_to_x_in_degrees = numpy.arccos ( v * chimera.Vector(1,0,0) ) * 180 / numpy.pi hope that helps... Greg On Nov 5, 2007 3:24 PM, <hsosa@aecom.yu.edu> wrote:
Hi, I have a couple of questions:
Is there a simple way to determine the angle between any of the three axes, X,Y or Z and the line connecting two selected atoms?. I know you can use the Angles/Torsions tools to determine the angle formed between 3 sets of atoms, but I wonder if you could use that tool, or some other, to report the angle of two atoms with the axes?.
Is it possible to draw a box with the axes around a structure as it can be done with a volume ?.
Thanks
Hernando
-- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa@aecom.yu.edu -----------------------------------
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Greg, Yes that is what I meant. My questions now is: Is it possible in idle to get the atoms being currently selected on the structure display window instead of explicitily writing their number ? i.e. Is there a command like: at1 = XXX.Current_selection_on_screen.atoms()[0] instead of: at1 = chimera.selection.OSLSelection(":32.A@CA").atoms()[0] Thanks Hernando Greg Pintilie wrote:
If you think of the line connecting the two atoms as a vector (with no position in space), then it's angle to another vector (e.g. the x-axis (1,0,0)) can be computed from the definition of dot product:
u . v = |u| * |v| * cos ( theta)
where u . v is the dot product between the vectors u and v, theta is the angle between the vectors u and v, and |u| is the magnitude (length) of u
so
cos ( theta) = u . v / ( |u| * |v| ) theta = arccos ( u.v / ( |u| * |v| ) )
if the vectors u and v are normalized / have unit length of 1 then you can simplify:
theta = arccos ( u.v )
within chimera, in the python interpreter IDLE, you first need to get the coordinates of the two atoms, for example, to get the vector from the alpha carbon in residue 32 to the alpha carbon in residue 33:
at1 = chimera.selection.OSLSelection(":32.A@CA").atoms()[0] at2 = chimera.selection.OSLSelection(":33.A@CA").atoms()[0] v = at2.coord() - at1.coord() v.normalize() import numpy theta_to_x_in_degrees = numpy.arccos ( v * chimera.Vector(1,0,0) ) * 180 / numpy.pi
hope that helps...
Greg
On Nov 5, 2007 3:24 PM, <hsosa@aecom.yu.edu> wrote:
Hi, I have a couple of questions:
Is there a simple way to determine the angle between any of the three axes, X,Y or Z and the line connecting two selected atoms?. I know you can use the Angles/Torsions tools to determine the angle formed between 3 sets of atoms, but I wonder if you could use that tool, or some other, to report the angle of two atoms with the axes?.
Is it possible to draw a box with the axes around a structure as it can be done with a volume ?.
Thanks
Hernando
-- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa@aecom.yu.edu -----------------------------------
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa@aecom.yu.edu -----------------------------------
yes, try: chimera.selection.currentAtoms() this will return a list of the currently selected atoms in the Chimera viewer. For your purposes, it sounds like you want vectors between every two atoms that you subsequently select. Watch out however, that the list returned by the above command need not be in the order that you made the selection. I noticed that in general the selection routines return atoms in arbitrary order, independent of the selection order or their position in the structure. Not sure if there is any way to enforce any kind of order? I would get around this by making the list manually: list = [] list = list + [chimera.selection.OSLSelection(":32.A@CA").atoms()[0], chimera.selection.OSLSelection(":33.A@CA").atoms()[0] ] list = list + [chimera.selection.OSLSelection(":34.A@CA").atoms()[0], chimera.selection.OSLSelection(":35.A@CA").atoms()[0] ] ... you can get the atom names and residues they're in easily of course by putting the mouse over them in the viewer a good thing about that is if you put the above in a script you'll have it available for later if you ever want to redo the measurements then you can compute angles between each vector by using a loop: import numpy for atoms in alist : v = atoms[1].coord() - atoms[0].coord() v.normalize() theta_to_x_in_degrees = numpy.arccos (v * chimera.Vector(1,0,0))*180/numpy.pi print "Res %d Atom %s to Res %d Atom %s angle to X-axis: %f" % (atoms[0].residue.id.position, atoms[0].name, atoms[1].residue.id.position, atoms[1].name, theta_to_x_in_degrees ) Greg On Nov 6, 2007 10:05 AM, <hsosa@aecom.yu.edu> wrote:
Hi Greg,
Yes that is what I meant. My questions now is: Is it possible in idle to get the atoms being currently selected on the structure display window instead of explicitily writing their number ?
i.e.
Is there a command like:
at1 = XXX.Current_selection_on_screen.atoms()[0]
instead of:
at1 = chimera.selection.OSLSelection(":32.A@CA").atoms()[0]
Thanks
Hernando
Greg Pintilie wrote:
If you think of the line connecting the two atoms as a vector (with no position in space), then it's angle to another vector (e.g. the x-axis (1,0,0)) can be computed from the definition of dot product:
u . v = |u| * |v| * cos ( theta)
where u . v is the dot product between the vectors u and v, theta is the angle between the vectors u and v, and |u| is the magnitude (length) of u
so
cos ( theta) = u . v / ( |u| * |v| ) theta = arccos ( u.v / ( |u| * |v| ) )
if the vectors u and v are normalized / have unit length of 1 then you can simplify:
theta = arccos ( u.v )
within chimera, in the python interpreter IDLE, you first need to get the coordinates of the two atoms, for example, to get the vector from the alpha carbon in residue 32 to the alpha carbon in residue 33:
at1 = chimera.selection.OSLSelection(":32.A@CA").atoms()[0] at2 = chimera.selection.OSLSelection(":33.A@CA").atoms()[0] v = at2.coord() - at1.coord() v.normalize() import numpy theta_to_x_in_degrees = numpy.arccos ( v * chimera.Vector(1,0,0) ) * 180 / numpy.pi
hope that helps...
Greg
On Nov 5, 2007 3:24 PM, <hsosa@aecom.yu.edu> wrote:
Hi, I have a couple of questions:
Is there a simple way to determine the angle between any of the three axes, X,Y or Z and the line connecting two selected atoms?. I know you can use the Angles/Torsions tools to determine the angle formed between 3 sets of atoms, but I wonder if you could use that tool, or some other, to report the angle of two atoms with the axes?.
Is it possible to draw a box with the axes around a structure as it can be done with a volume ?.
Thanks
Hernando
-- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa@aecom.yu.edu -----------------------------------
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
--
----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa@aecom.yu.edu -----------------------------------
On Nov 6, 2007, at 7:38 AM, Greg Pintilie wrote:
yes, try:
chimera.selection.currentAtoms()
this will return a list of the currently selected atoms in the Chimera viewer.
For your purposes, it sounds like you want vectors between every two atoms that you subsequently select. Watch out however, that the list returned by the above command need not be in the order that you made the selection. I noticed that in general the selection routines return atoms in arbitrary order, independent of the selection order or their position in the structure. Not sure if there is any way to enforce any kind of order?
chimera.selection.currentAtoms(ordered=True) This returns the atoms in the order they were selected. It's not the default since it involves a possibly-expensive sorting operation and because many uses of the current selection don't care about the ordering. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
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