Hi, I have a DNA model which is composed of two DNA duplexes. I want to measure the angle between the two duplexes and if there a way to do it in PHENIX or in other software? Thanks you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：[email protected]
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello Xiang, 3dna (www.x3dna.org) is the program of choice for this. Unfortunately the documentation on the above new web-site is difficult to find, but the downloaded software contains plenty of examples. You could also load the molecule into coot, place two atom (say A1+B1 and A2+B2) each to define the helix axes and calculate the cosine of the angle as the direct product of (A1-B1)/|A1-B1| and (A2-B2)/|A2-B2|. That's probably quicker and as accurate. Best, Tim On 01/20/2014 02:48 PM, ?? wrote:
Hi,
I have a DNA model which is composed of two DNA duplexes. I want to measure the angle between the two duplexes and if there a way to do it in PHENIX or in other software?
Thanks you very much for your help!
Sincerely, Xiang
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
- -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFS3TpmUxlJ7aRr7hoRAsZoAKDaP15avNrRb5cONgG2VLQwlCym0wCeOK69 uLoYIpdqzo9pxXYztinmIyI= =iPNS -----END PGP SIGNATURE-----
Hi Xiang, there is no ready-to-use tool for this right now, but I can spend a few moments and add one so it's available in next Phenix nightly build in a day or two. phenix.angle model.pdb selection="chain A and resseq 1:123" selection="chain B and resseq 20:345" The underlying procedure would do the following: - extract two sets of coordinates of atoms corresponding to two provided atom selections; - draw two optimal lines (LS fit) passing through the above sets of coordinates; - compute and report angle between those two lines? Would this be helpful? Is it worth adding such tool? Pavel On 1/20/14, 5:48 AM, ?? wrote:
Hi,
I have a DNA model which is composed of two DNA duplexes. I want to measure the angle between the two duplexes and if there a way to do it in PHENIX or in other software?
Thanks you very much for your help!
Sincerely, Xiang
-- Li Xiang Department of chemistry, Purdue University Email:[email protected] mailto:[email protected]
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Pavel,
For us DNA people (we clearly are a minority) I think this would be a very
useful addition. Either a script or as part of the GUI would be OK
Cheers
Jens
--
+++++++++++++++++++++++++++++++++++++++++++++++++++
Jens J. Birktoft
Director of Crystallography
Structural DNA Nanotechnology
New York University
e-mail: [email protected]; Phone: 212-749-5057
very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025
+++++++++++++++++++++++++++++++++++++++++++++++
On Mon, Jan 20, 2014 at 12:47 PM, Pavel Afonine
Hi Xiang,
there is no ready-to-use tool for this right now, but I can spend a few moments and add one so it's available in next Phenix nightly build in a day or two.
phenix.angle model.pdb selection="chain A and resseq 1:123" selection="chain B and resseq 20:345"
The underlying procedure would do the following: - extract two sets of coordinates of atoms corresponding to two provided atom selections; - draw two optimal lines (LS fit) passing through the above sets of coordinates; - compute and report angle between those two lines?
Would this be helpful? Is it worth adding such tool?
Pavel
On 1/20/14, 5:48 AM, 李翔 wrote:
Hi,
I have a DNA model which is composed of two DNA duplexes. I want to measure the angle between the two duplexes and if there a way to do it in PHENIX or in other software?
Thanks you very much for your help!
Sincerely, Xiang
-- Li Xiang Department of chemistry, Purdue University Email：[email protected]
_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
++++
Hi Jens,
Nice to see you in the email list here! I did no know hat before that you are in the list.:)
I think there is a way to measure the angles between alpha helixes for protein in pymol which should be somehow the similar for DNA. I am trying to wrap up the rest of the data so I asked a few questions here.
Sincerely,
Xiang
----- Original Message -----
From: jens j birktoft
Hi Xiang,
there is no ready-to-use tool for this right now, but I can spend a few moments and add one so it's available in next Phenix nightly build in a day or two.
phenix.angle model.pdb selection="chain A and resseq 1:123" selection="chain B and resseq 20:345"
The underlying procedure would do the following: - extract two sets of coordinates of atoms corresponding to two provided atom selections; - draw two optimal lines (LS fit) passing through the above sets of coordinates; - compute and report angle between those two lines?
Would this be helpful? Is it worth adding such tool?
Pavel
On 1/20/14, 5:48 AM, 李翔 wrote:
Hi,
I have a DNA model which is composed of two DNA duplexes. I want to measure the angle between the two duplexes and if there a way to do it in PHENIX or in other software?
Thanks you very much for your help!
Sincerely, Xiang
-- Li Xiang Department of chemistry, Purdue University Email：[email protected]
_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
++++
Hi Pavel,
Thanks a lot for the reply! I think it will be helpful for the guys work
with DNA like me. If I remember right, in Pymol there is a way to measure
the angles for alpha helices and it should very similar to calculate the
angles for DNA duplexes. But there is not a way to do it. It will great if
PHENIX can do the measurement like this.
Sincerely,
Xiang
2014/1/20 Pavel Afonine
Hi Xiang,
there is no ready-to-use tool for this right now, but I can spend a few moments and add one so it's available in next Phenix nightly build in a day or two.
phenix.angle model.pdb selection="chain A and resseq 1:123" selection="chain B and resseq 20:345"
The underlying procedure would do the following: - extract two sets of coordinates of atoms corresponding to two provided atom selections; - draw two optimal lines (LS fit) passing through the above sets of coordinates; - compute and report angle between those two lines?
Would this be helpful? Is it worth adding such tool?
Pavel
On 1/20/14, 5:48 AM, 李翔 wrote:
Hi,
I have a DNA model which is composed of two DNA duplexes. I want to measure the angle between the two duplexes and if there a way to do it in PHENIX or in other software?
Thanks you very much for your help!
Sincerely, Xiang
-- Li Xiang Department of chemistry, Purdue University Email：[email protected]
_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Li Xiang Department of chemistry, Purdue University Email：[email protected]
Pavel Afonine wrote: . .
The underlying procedure would do the following: - extract two sets of coordinates of atoms corresponding to two provided atom selections; - draw two optimal lines (LS fit) passing through the above sets of coordinates; - compute and report angle between those two lines?
This could be innacurate for very short helices (admittedly not the case one usually would be looking for angles), or determining the axis of a short portion of a curved helix. A more accurate way to determine the axis- have a long canonical duplex constructed with its axis along Z (0,0,1). Superimpose as many residues of that as required on the duplex being tested, using only backbone atoms or even only phosphates. Operate on (0,0,1) with the resulting operator (i.e. take the third column of the rotation matrix) and use that as a vector parallel to the axis of the duplex being tested.
Hi Ed, interesting idea! Although I was thinking to have a tool that is a little more general and a little less context dependent. Say you have two clouds of points that are (thinking in terms of macromolecules) two alpha helices (for instance), and you want to know the angle between the axes of the two helices. How would I approach this?.. First, for each helix I would compute a symmetric 3x3 matrix like this: sum(xn-xc)**2 sum(xn-xc)*(yn-xc) sum(xn-xc)*(zn-zc) sum(xn-xc)*(yn-xc) sum(yn-yc)**2 sum(yn-yc)*(yz-zc) sum(xn-xc)*(zn-zc) sum(yn-yc)*(yz-zc) sum(zn-zc)**2 where (xn,yn,zn) is the coordinate of nth atom, the sum is taken over all atoms, and (xc,yc,zc) is the coordinate of the center of mass. Second, for each of the two matrices I would find its eigen-values and eigen-vectors, and select eigen-vectors corresponding to largest eigenvalues. Finally, the desired angle is the angle between the two eigen-vectors found above, which is computed trivially. I think this a little simpler than finding the best fit for a 3D line. What you think? Pavel On 1/20/14, 2:14 PM, Edward A. Berry wrote:
Pavel Afonine wrote: . .
The underlying procedure would do the following: - extract two sets of coordinates of atoms corresponding to two provided atom selections; - draw two optimal lines (LS fit) passing through the above sets of coordinates; - compute and report angle between those two lines?
This could be innacurate for very short helices (admittedly not the case one usually would be looking for angles), or determining the axis of a short portion of a curved helix. A more accurate way to determine the axis- have a long canonical duplex constructed with its axis along Z (0,0,1). Superimpose as many residues of that as required on the duplex being tested, using only backbone atoms or even only phosphates. Operate on (0,0,1) with the resulting operator (i.e. take the third column of the rotation matrix) and use that as a vector parallel to the axis of the duplex being tested. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Pavel, that's the method described in http://journals.iucr.org/a/issues/2011/01/00/sc5036/index.html ;-) based on the moments of inertia (a computer scientist might name it differently). I am not sure, though, you would get the desired result for short helices. E.g. a helix defined by three atoms the eigenvalue would point roughly in the direction of the external phosphates, which is far from parallel with the helix axis. Best, Tim On 01/21/2014 04:20 AM, Pavel Afonine wrote:
Hi Ed,
interesting idea! Although I was thinking to have a tool that is a little more general and a little less context dependent. Say you have two clouds of points that are (thinking in terms of macromolecules) two alpha helices (for instance), and you want to know the angle between the axes of the two helices. How would I approach this?..
First, for each helix I would compute a symmetric 3x3 matrix like this:
sum(xn-xc)**2 sum(xn-xc)*(yn-xc) sum(xn-xc)*(zn-zc) sum(xn-xc)*(yn-xc) sum(yn-yc)**2 sum(yn-yc)*(yz-zc) sum(xn-xc)*(zn-zc) sum(yn-yc)*(yz-zc) sum(zn-zc)**2
where (xn,yn,zn) is the coordinate of nth atom, the sum is taken over all atoms, and (xc,yc,zc) is the coordinate of the center of mass.
Second, for each of the two matrices I would find its eigen-values and eigen-vectors, and select eigen-vectors corresponding to largest eigenvalues.
Finally, the desired angle is the angle between the two eigen-vectors found above, which is computed trivially. I think this a little simpler than finding the best fit for a 3D line.
What you think?
Pavel
On 1/20/14, 2:14 PM, Edward A. Berry wrote:
Pavel Afonine wrote: . .
The underlying procedure would do the following: - extract two sets of coordinates of atoms corresponding to two provided atom selections; - draw two optimal lines (LS fit) passing through the above sets of coordinates; - compute and report angle between those two lines?
This could be innacurate for very short helices (admittedly not the case one usually would be looking for angles), or determining the axis of a short portion of a curved helix. A more accurate way to determine the axis- have a long canonical duplex constructed with its axis along Z (0,0,1). Superimpose as many residues of that as required on the duplex being tested, using only backbone atoms or even only phosphates. Operate on (0,0,1) with the resulting operator (i.e. take the third column of the rotation matrix) and use that as a vector parallel to the axis of the duplex being tested. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Dear Tim and Pavel, It sounds logical to start from a formal geometrical definition WHAT IS a helix axis for ANY helix, in particular a short one (since this looks like the point of discussion). And to address the original question after expressing this formal definition mathematically. Best regards, Sacha Urzhumtsev -----Message d'origine----- De : [email protected] [mailto:[email protected]] De la part de Tim Gruene Envoyé : mardi 21 janvier 2014 10:25 À : [email protected] Objet : Re: [phenixbb] measuring the angle between two DNA duplexes Hi Pavel, that's the method described in http://journals.iucr.org/a/issues/2011/01/00/sc5036/index.html ;-) based on the moments of inertia (a computer scientist might name it differently). I am not sure, though, you would get the desired result for short helices. E.g. a helix defined by three atoms the eigenvalue would point roughly in the direction of the external phosphates, which is far from parallel with the helix axis. Best, Tim
One way that I've used for alpha-helices is to start with an ideal model with it's axis along say z, then get the rotation required to fit the ideal helix to the model. This works even for short helices
Phil
On 21 Jan 2014, at 09:25, Tim Gruene
Hi Pavel,
that's the method described in http://journals.iucr.org/a/issues/2011/01/00/sc5036/index.html ;-) based on the moments of inertia (a computer scientist might name it differently). I am not sure, though, you would get the desired result for short helices. E.g. a helix defined by three atoms the eigenvalue would point roughly in the direction of the external phosphates, which is far from parallel with the helix axis.
Best, Tim
On 01/21/2014 04:20 AM, Pavel Afonine wrote:
Hi Ed,
interesting idea! Although I was thinking to have a tool that is a little more general and a little less context dependent. Say you have two clouds of points that are (thinking in terms of macromolecules) two alpha helices (for instance), and you want to know the angle between the axes of the two helices. How would I approach this?..
First, for each helix I would compute a symmetric 3x3 matrix like this:
sum(xn-xc)**2 sum(xn-xc)*(yn-xc) sum(xn-xc)*(zn-zc) sum(xn-xc)*(yn-xc) sum(yn-yc)**2 sum(yn-yc)*(yz-zc) sum(xn-xc)*(zn-zc) sum(yn-yc)*(yz-zc) sum(zn-zc)**2
where (xn,yn,zn) is the coordinate of nth atom, the sum is taken over all atoms, and (xc,yc,zc) is the coordinate of the center of mass.
Second, for each of the two matrices I would find its eigen-values and eigen-vectors, and select eigen-vectors corresponding to largest eigenvalues.
Finally, the desired angle is the angle between the two eigen-vectors found above, which is computed trivially. I think this a little simpler than finding the best fit for a 3D line.
What you think?
Pavel
On 1/20/14, 2:14 PM, Edward A. Berry wrote:
Pavel Afonine wrote: . .
The underlying procedure would do the following: - extract two sets of coordinates of atoms corresponding to two provided atom selections; - draw two optimal lines (LS fit) passing through the above sets of coordinates; - compute and report angle between those two lines?
This could be innacurate for very short helices (admittedly not the case one usually would be looking for angles), or determining the axis of a short portion of a curved helix. A more accurate way to determine the axis- have a long canonical duplex constructed with its axis along Z (0,0,1). Superimpose as many residues of that as required on the duplex being tested, using only backbone atoms or even only phosphates. Operate on (0,0,1) with the resulting operator (i.e. take the third column of the rotation matrix) and use that as a vector parallel to the axis of the duplex being tested. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen
GPG Key ID = A46BEE1A
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Tim, thanks for the reference! There is a number of instances where this approach is useful. In Phenix this is also used to determine density map peak sphericity (see cctbx/maptbx/sphericity.h) and to get initial values for refinement of anisotropic ADPs from map peaks. Sure I will play with this and visit as many corner cases as I could think of! All the best, Pavel On 1/21/14, 1:25 AM, Tim Gruene wrote:
Hi Pavel,
that's the method described in http://journals.iucr.org/a/issues/2011/01/00/sc5036/index.html ;-) based on the moments of inertia (a computer scientist might name it differently). I am not sure, though, you would get the desired result for short helices. E.g. a helix defined by three atoms the eigenvalue would point roughly in the direction of the external phosphates, which is far from parallel with the helix axis.
Best, Tim
On 01/21/2014 04:20 AM, Pavel Afonine wrote:
Hi Ed,
interesting idea! Although I was thinking to have a tool that is a little more general and a little less context dependent. Say you have two clouds of points that are (thinking in terms of macromolecules) two alpha helices (for instance), and you want to know the angle between the axes of the two helices. How would I approach this?..
First, for each helix I would compute a symmetric 3x3 matrix like this:
sum(xn-xc)**2 sum(xn-xc)*(yn-xc) sum(xn-xc)*(zn-zc) sum(xn-xc)*(yn-xc) sum(yn-yc)**2 sum(yn-yc)*(yz-zc) sum(xn-xc)*(zn-zc) sum(yn-yc)*(yz-zc) sum(zn-zc)**2
where (xn,yn,zn) is the coordinate of nth atom, the sum is taken over all atoms, and (xc,yc,zc) is the coordinate of the center of mass.
Second, for each of the two matrices I would find its eigen-values and eigen-vectors, and select eigen-vectors corresponding to largest eigenvalues.
Finally, the desired angle is the angle between the two eigen-vectors found above, which is computed trivially. I think this a little simpler than finding the best fit for a 3D line.
What you think?
Pavel
On 1/20/14, 2:14 PM, Edward A. Berry wrote:
Pavel Afonine wrote: . .
The underlying procedure would do the following: - extract two sets of coordinates of atoms corresponding to two provided atom selections; - draw two optimal lines (LS fit) passing through the above sets of coordinates; - compute and report angle between those two lines?
This could be innacurate for very short helices (admittedly not the case one usually would be looking for angles), or determining the axis of a short portion of a curved helix. A more accurate way to determine the axis- have a long canonical duplex constructed with its axis along Z (0,0,1). Superimpose as many residues of that as required on the duplex being tested, using only backbone atoms or even only phosphates. Operate on (0,0,1) with the resulting operator (i.e. take the third column of the rotation matrix) and use that as a vector parallel to the axis of the duplex being tested. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi, Pavel, Yes, my suggestion would be specific for double-stranded nucleic acid. A separate but similar one would be required for protein (I've written and used that one). For protein the bf straight line would not be so good because its a single helix, so at the end atoms are on only one side. Say you have 1.5 turns of helix. the best fit line would be skewed to go through the ends of the backbone (as Tim Gruene noted). For a double helix it would be less of a problem since you have one chain on each side of the axis to balance. But in the extreme, say when the length is less than the thickness (i.e. a disk), the best-fit line could be closer to the diameter than the axis. I wouldn't pretend to advise you on programming linear algerba, but for my own edification I will study your matrix and try to understand, with help from the page Tim linked. At first glance it looks like S.V. decomposition on n vectors in 3 space, or 3 vectors in N space, where the singular vectors, values are taken as the eigenvectors, values of the matrix U'V or UV'. Or the normal equations for solving a least-squares problem with a generalized inverse involving [M'M]^-1 but then you would go on to invert the matrix rather than finding its eigenvectors. Pavel Afonine wrote:
Hi Ed,
interesting idea! Although I was thinking to have a tool that is a little more general and a little less context dependent. Say you have two clouds of points that are (thinking in terms of macromolecules) two alpha helices (for instance), and you want to know the angle between the axes of the two helices. How would I approach this?..
First, for each helix I would compute a symmetric 3x3 matrix like this:
sum(xn-xc)**2 sum(xn-xc)*(yn-xc) sum(xn-xc)*(zn-zc) sum(xn-xc)*(yn-xc) sum(yn-yc)**2 sum(yn-yc)*(yz-zc) sum(xn-xc)*(zn-zc) sum(yn-yc)*(yz-zc) sum(zn-zc)**2
where (xn,yn,zn) is the coordinate of nth atom, the sum is taken over all atoms, and (xc,yc,zc) is the coordinate of the center of mass.
Second, for each of the two matrices I would find its eigen-values and eigen-vectors, and select eigen-vectors corresponding to largest eigenvalues.
Finally, the desired angle is the angle between the two eigen-vectors found above, which is computed trivially. I think this a little simpler than finding the best fit for a 3D line.
What you think?
Pavel
On 1/20/14, 2:14 PM, Edward A. Berry wrote:
Pavel Afonine wrote: . .
The underlying procedure would do the following: - extract two sets of coordinates of atoms corresponding to two provided atom selections; - draw two optimal lines (LS fit) passing through the above sets of coordinates; - compute and report angle between those two lines?
This could be innacurate for very short helices (admittedly not the case one usually would be looking for angles), or determining the axis of a short portion of a curved helix. A more accurate way to determine the axis- have a long canonical duplex constructed with its axis along Z (0,0,1). Superimpose as many residues of that as required on the duplex being tested, using only backbone atoms or even only phosphates. Operate on (0,0,1) with the resulting operator (i.e. take the third column of the rotation matrix) and use that as a vector parallel to the axis of the duplex being tested. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hello, next nightly build of Phenix should have this available in the command line (It's up to Nat when (and if) it's going to be available in the GUI). *phenix.angle:* Given PDB file and two atom selections that allow to define two lines compute the angle between these two lines. If atom selection defines two points then the line is defined uniquely and passes through these points. If atom selection defines more than two points then line coincides with the longest axis of the cloud of points. *Example 1:* two pairs of points are given to define two axes: phenix.angle model.pdb "chain A and (resseq 1 and name CA or resseq 2 and name CA)" "chain B and (resseq 1 and name CA or resseq 2 and name CA)" Above, selection "chain A and (resseq 1 and name CA or resseq 2 and name CA)" selects two C-alpha atoms in residues 1 and 2 in chain A. Analogously, "chain B and (resseq 1 and name CA or resseq 2 and name CA)" selects two C-alpha atoms in residues 1 and 2 in chain B. Both atom selections define two lines, and the angle between these lines is output. *Example 2:* phenix.angle model.pdb "chain A" "chain B" Here "chain A" selects all atoms in chain A, similarly second selection does for chain B. *More Phenix atom selection syntax and examples:* http://www.phenix-online.org/documentation/refinement.htm#anch370 *Under the hood:* If provided atom selections specify four points - two for each axis, then the angle is computed trivially. If provided atom selections specify more than two points to define axis, then the following is done: 1) Select atoms corresponding to two selections; 2) Assign selected atoms occupancy=1 and B=20, and move atoms into an orthorhombic box; 3) Compute two Fourier maps of 4A resolution (perhaps 6A is even better!) corresponding to two sets of selected atoms; 4) Sigma-scale each synthesis, and truncate {m=0, if m<1, else m=m}; 5) For each of the two maps compute symmetric 3x3 matrix like this: sum(xn-xc)**2 sum(xn-xc)*(yn-xc) sum(xn-xc)*(zn-zc) sum(xn-xc)*(yn-xc) sum(yn-yc)**2 sum(yn-yc)*(yz-zc) sum(xn-xc)*(zn-zc) sum(yn-yc)*(yz-zc) sum(zn-zc)**2 where (xn,yn,zn) is the coordinate of nth grid point, the sum is taken over all grid points in within the radius that is equal to the half of max length of the selected set of atoms, and (xc,yc,zc) is the coordinate of the center of mass. Each some above is weighted by map value. 6) For each of the two matrices I would find its eigen-values and eigen-vectors, and select eigen-vectors corresponding to largest eigenvalues. 7) The desired angle is the angle between the two eigen-vectors found in step 6. This may seem a bit convoluted but actual calculations take a fraction of a second, and the underlying code is just about 130 lines (including i/o and documentation page). For those liking to dig in the code, the tests that exercise phenix.angle can be found here: cctbx_project/mmtbx/regression/tst_phenix_angle.py which basically define the scope of problems that I used so far to exercise the tool. I notices that a minimal fraction of a helix need to contain at least 5-6 residues: this typically provides 5% accuracy (of calculated angle using the above procedure compared to the known answer). Please let me know of any problems, bugs, feature requests and suggestions etc *off-list*. Pavel On 1/20/14, 5:48 AM, ?? wrote:
Hi,
I have a DNA model which is composed of two DNA duplexes. I want to measure the angle between the two duplexes and if there a way to do it in PHENIX or in other software?
Thanks you very much for your help!
Sincerely, Xiang
-- Li Xiang Department of chemistry, Purdue University Email:[email protected] mailto:[email protected]
participants (8)
-
Alexandre OURJOUMTSEV -
Edward A. Berry -
jens j birktoft -
Pavel Afonine -
Phil Evans -
Tim Gruene -
Xiang Li -
李翔