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
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
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
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:
>
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,
