Just use the "rms_cur" command instead of "align".
https://pymolwiki.org/index.php/rms_cur
Cheers,
Thomas
> On Aug 28, 2017, at 10:04 AM, Johannes Sommerkamp
> <155b9e78396e-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Thanks a lot for your answers and the PyMOL mailing list hint. I didnt
Or using cctbx:
from scitbx.array_family import flex
import iotbx.pdb
def run():
xyz_1 = iotbx.pdb.input(file_name="file_1.pdb").atoms().extract_xyz()
xyz_2 = iotbx.pdb.input(file_name="file_2.pdb").atoms().extract_xyz()
print flex.mean(flex.sqrt((xyz_1 - xyz_2).dot()))
if (__name__
I should learn not to post while distracted. That last line was both
over-engineered, and wrong. What you want is:
rmsd = sum(numpy.linalg.norm(xyz1-xyz2, axis=1))/len(xyz1)
On 2017-08-28 14:32, Tristan Croll wrote:
In this case calculating the rmsd is easy:
- get the coordinates of each
Look at CCP4 "compar"
By default it averages RMSD over all atoms in mainchain and sidechain
of the residue, but if you first awk out only CA (or use pdbset to pick CA)
foreach structure, the mainchain value will presumably be the
Euclidian CA distance (This may require identical sequences,
at
Dear Carlos,
You are correct. I reinstalled CCP4 two days ago and also got version
0044 and that did not incude the new shelxe_2017-1. However the new
shelxe is definitely on the shelx server. It is a single statically
linked executable with no dependencies (!) so you can simply replace the
In this case calculating the rmsd is easy:
- get the coordinates of each structure as n x 3 numpy arrays. The Pymol
commands for this should look like:
xyz1 = cmd.get_coords('sele1', 1)
xyz2 = cmd.get_coords('sele2', 1)
Then,
rmsd = numpy.linalg.norm(numpy.sqrt((xyz1-xyz2)**2), axis=1)
Thanks a lot for your answers and the PyMOL mailing list hint. I didnt
had in mind this list.
I read the Pymol Wiki. The commands
align moving, target, cycles=0, transform=0
align moving, target, cycles=0
give identical values for RMSD. So, the only difference is, that the
moving
