Hrellow James.

You could do it like this:


fetch 2yh2, async=0
fetch 3zwq, async=0

super 3zwq, 2yh2

print cmd.get_names("objects")
print cmd.get_names("public_objects")

my_objects = cmd.get_names("public_objects")

for i in range(len(my_objects)):
   cmd.create("my_protein", my_objects[i], 1, (i+1))
python end

show_as cartoon, my_protein
save my_protein.pdb, my_protein, state=0
set movie_fps, 1

Troels Emtekær Linnet
Ved kløvermarken 9,
2300 København S
+45 60210234

2012/9/23 James Starlight <>
Dear PyMol users!

I've already created such topic and found sollution to it but now I
forgot how exactly I did it :)

The main task is the creation of the trajectory in NMR-like format
from initial X-ray structures ( each of them is the indivixual
snapshot for suture trajectory).
E.g in Pymol I have opened 15 x-ray structures aligned against one
reference. All of that structures also consist of different numbers of
states (models). As the result I want to chose only first state from
each of that structures and create new common pdb file consisted of
each structure (total 15 snapshots). Its important that In that new
NMR-like file order of the models must be corresponded to the order of
structures in the PyMol window. How I could do that?

Thanks for help


Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:;258768047;13503038;j?
PyMOL-users mailing list (
Info Page: