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
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
Hi Johannes,
Did you read the PymoWIKI entry on the align command?
https://pymolwiki.org/index.php/Align#RMSD
I think this should give you what you want within PyMOL.
Btw, there is a nice dedicated PyMOL mailing list
https://pymolwiki.org/index.php/PyMOL_mailing_list
It is rather low traffic,
May be you should try pdbefold server. It provides rmsd between equivalent
CA atoms of superimposed structures.
All the best.
Vipul Panchal,
Ph.D. student
CSIR-IGIB
(M)- 091 7678617949
On 27-Aug-2017 4:50 PM, "Johannes Sommerkamp" <
155b9e78396e-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hello
Hello everybody,
I have superposed two structures based on the central beta-sheet CA
atoms with the "super" command in Pymol.
Now, I want to calculate the RMSD between ALL atoms or ALL CA atoms
without moving the structures again. The rms_cur command in Pymol would
do that, but only works if
