Hi Thomas and David,
Thanks for bringing this to my attention. PyMOL was indeed trying to
fit to a degenerate case. I fixed the bug: PyMOL will now print:
ExecutiveAlign: No alignment found.
and leave your objects untouched.
This fix is mixed in with some other development code, so I'll extr
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 them.
Hi,
On Wed, 22 Sep 2010 23:29:14 -0400 Jason Vertrees
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 in this email:
http://ww
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,
Th
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 sel
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 ex
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... S
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):
>
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
de
Hi Ramiro,
A bit of linear algebra wouldn't hurt... :p
In python:
def vsub(a,b): return a[0]-b[0], a[1]-b[1], a[2]-b[2]
def dot(a,b): return a[0]*b[0]+a[1]*b[1]+a[2]*b[2]
def svmul(s,a): return s*a[0], s*a[1], s*a[2]
def normalize(a): return svmul(1/math.sqrt(dot(a,a)),a)
def cross(a,b): retu
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
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 t
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
lin
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
li
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
get
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