Jenna,
Use PyMOL to download the biological unit:
fetch 1b8e, type=pdb1
split the states out (you'll notice it's a two-state object)
split_states 1b8e
You can also create symmetry expansion via, A > Generate > Symmetry Mates >
within X A, from your original object.
Cheers,
-- Jason
On Tue,
Hello Jenna,
On Tue, 06 Apr 2010 00:36:38 -0400 JiangJiang Liu wrote:
> When I open the pdb file 1B8E (a homodimer protein) through
> pymol I can only see a monomer shown in the screen. Now I know the
> biological dimer is produced through crystallographic symmetry operations
> in
Hi Rob, Jenna,
Be aware that the symmetry data (symexp) need not be equal to the
biological unit transformations (remark biomt), even though it will
often match.
And since I'm posting anyway, here's another possibility:
load 1b8e.pdb, A
create B,A
alter_state 1,B,(x,y,z)=(-x,y,33.43-z)
Cheers,
Dear Tsherk :
Thank you so much for your reply on my pymol question. Your suggestions are
helpful to solve the question that has been confused me for so long.
I still have another related question. After I created the dimmer
structure, do you know how to save the new structure as a pdb fi
Hi Jenna,
I think you already managed (using 'save'). And of course there are
two times as many coordinates in a dimer, so the saved file will be
twice the size. By the way, before saving, you might want to make sure
the chains get different chain IDs, so you can easily address them
later:
alter
