Hello Mat,
Thank you for your reply.
I followed your codes in the second line and get a series of output, which look
like:
(9.949092864990234, 267, 0, 9.949092864990234, 267, 420.0, 226)
I guess the first and the fourth float numbers are the rmsd, but what are other
numbers in the line?
Best
It appears that customs labels created with
pseudoatom labelname, pos=[x,y,z], label=some_string
lose their colors when the image is raytraced.
Does anyone know whether a workaround exist?
Thanks.
Fred
[32m***
Fred
Superpose all states of an object to one of the states.
print cmd.intra_fit("my-trajCA", 1)Do the same, but this time the
target/reference is a different object.
for s in range(cmd.count_states()): print(cmd.align('my-traj', 'ref',
mobile_state=s + 1, target_state=1, cycles=0, transform=0))
On
There is also intra_rms and instra_fit commands:
https://pymol.org/pymol-command-ref.html#intra_rms
https://pymol.org/pymol-command-ref.html#intra_fit
For example:
intra_fit name CA and resid 1326-1350, 0
Maybe they will be useful.
Best, Mat
On Mon, 19 Aug 2019 at 13:54, sunyeping wrote:
> He
Hello Mateusz,
Thank you very much for your reply to my inquiry. Before I try the PyMOL
extension you mentioned, I want to try scripting language in pymol. I wrote a
attemptive one (align.py):
cmd.load("A.gro")
cmd.load("A.xtc")
cmd.load("ref.pdb")
for i in range(1, 5001):
cmd.align(ref, A,t
Hi Sunyeping,
Besides using the scripting language in pymol, you might want to consider
the experimental PyMOL extension created by the PyMOL Fellows (me and Paul
Smith, https://pymol.org/fellowship/). The extension relies on the
MDAnalysis package and so far includes RMSD as an example. Here is t
Dear everyall,
I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames and
a reference structure (B.pdb) into pymol. I wish to get the rmsd value between
each state of the MD simulation trajectory and the reference structure, but I
don't know how. I can use the align command
