Hi,
I have two chemically identical molecules, but with different residue names,
residue numbers and atom numbers. However the atom coordinates are also
different. Is there some script that could map down the atom names, residue
names and numbers to each other?
Thanks for any ideas!
Krisztina
Hi all,
In pymol. does it possible to smooth some of the loops in a structure?
I use command:
set cartoon_smooth_loop=1, 10g3a and c. L
the software give me:
Setting: cartoon_smooth_loops set for 1640 atoms in object "10g3a".
But there is nothing changed in the image window.
Many thanks!
yam
Hi Yamei,
The cartoon_smooth_loops setting is an object-based setting, so it
cannot be done as you're attempting.
You can do some finagling though to get close:
# fetch a protein
fetch 1rx1, async=0
# show it as cartoon
as cartoon
# select a region to hide
select to_hide, i. 116-132
# cre
Hi All,
I'm trying to manually model a linker region using computational
information (such as which residues are predicted to be in helical form,
etc.). I have the sequence in PyMOL as an unmodeled linear chain (or
whatever the program chose to do with bond angles when I manually generated
the seq
Hi Alex,
To alter secondary structure properties of atoms use the alter command:
# make all atoms in the my_helix selection become alpha helices
alter my_helix, ss='h'
PyMOL will only draw, to the best of its ability, the helical
representation. It will not adjust the atom coordinates for you.
