Hi David,
this is bug, indeed. I also hit this some time ago but didn't report it
so far. The actual problem is that the cmd.super('1acb', '426d') fails
completely and only aligns a single atom, resulting in a Null-matrix
that collapses all of 1acb into a single point. The RMSD of 2.8 that you
Hi everyone and thanks for reading this!
I am interested in measuring the angle between aromatic ring planes.
Is there any easy way/script to do it?
One way that came to my mind is creating a pseudoatom representing the
centroid for each ring (I already know how to do that), then drawing two
Hi everyone and thanks for reading this!
I am interested in measuring the angle between aromatic ring planes.
Is there any easy way/script to do it?
One way that came to my mind is creating a pseudoatom representing the
centroid for each ring (I already know how to do that), then drawing two
Hi Ramiro,
Assuming your rings are nicely planar, and representing the ring as:
1-2-3
| |
6-5-4
you can get the plane normal vector as the vector cross product from
(3)-(1) and (5)-(1).
Doing so for both rings gives you the two normal vectors. The angle
then follows from the dot product of
Thanks for your kind help, Tsjerk.
Hi Ramiro,
Assuming your rings are nicely planar, and representing the ring as:
1-2-3
| |
6-5-4
you can get the plane normal vector as the vector cross product from
(3)-(1) and (5)-(1).
OK. But I just started to use pymol. Which are the commands
no need to implement common linear algebra functions, there is the
chempy.cpv module shipped with pymol (and there is numpy as well).
Ramiro, I recently did something similar, just adjust the residue
selection in the code below (requires numpy):
python
from chempy import cpv
import numpy, math
Thanks very much Thomas for your help.
no need to implement common linear algebra functions, there is the
chempy.cpv module shipped with pymol (and there is numpy as well).
Ramiro, I recently did something similar, just adjust the residue
selection in the code below (requires numpy):
I
Hi Thomas,
You're right, and using an svd on the whole ring is also more correct.
But the vector stuff is simple and handy to have lying around, and it
serves also to give some insight in what's going on :)
numpy.linalg.svd is magic if you don't know how a cross product or
normalization works...
Hi Ramiro,
* How do I adjust the code with my selected rings? Do I need to include
both residues in the same selection in pymol, then rename the selection,
and then include the chosen selection name in the code where you write
selection?
you need two selections of two residues, in my example
Hi Ramiro,
Another option is to fit (in a least-squares sense) a plane to each of
your rings and then calculate the angle between the fitted planes'
normals. This would help if your rings are not perfectly planar: it
would spread the deviation among all atoms in the ring not just the
ones you
On Thu, 2010-09-23 at 09:54 -0400, Jason Vertrees wrote:
Hi Ramiro,
Another option is to fit (in a least-squares sense) a plane to each of
your rings and then calculate the angle between the fitted planes'
normals.
that's what the recently posted ring_angle.py script does.
Cheers,
Thomas
Hi,
On Wed, 22 Sep 2010 23:29:14 -0400 Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi Mark,
We used to be able to call this to get the viewport size. But,
somewhere along the line Warren removed this. I'll see if I can add
it back in, or find out why he removed it.
As mentioned
Hi Renuka,
Please keep all PyMOL-related correspondence on the mailing list. That way,
other people can find the answers by reading the mailing list or searching
the web.
Your task is now getting a little more complicated. I think you'll probably
want to define some Python functions and use
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