Hello!
I am working on aligning two 3D PDB structures. I have
followed the instructions on the Jalview 2.8.2 Manual and Tutorial as
follows:
Exercise 15: Aligning
structures using the ferredoxin sequence alignment.
15.a. Continue
with the Jalview project created in exercise 14. Use the Discover PDB IDs
function to retrieve PDB IDs associated with the FER1_MAIZE sequence.
15.b. Once
discovery has completed, use the View PDB Structure submenu to view the
PDB file associated with FER1_MAIZE. Jalview will give you the option of
aligning
the structure to the one already open. To superimpose the structure associated
with
FER1_MAIZE with the one associated with FER1_SPIOL, press the Yes button.
The Jmol view will update to show both structures, and one will be moved on to
the
other. If this doesn’t happen, use the Align function in the Jmol submenu
15.c. Create a new view on the
alignment, and hide all but columns 121 through to 132.
15.d. Use the Jmol submenu to
recompute the superposition using just columns 121-132 of
the alignment.
Note how the molecules shift
position when superposed using a short part of the two
structures.
15.e. Compare the initial and
final RMSDs for superimposing molecules with the small
section and with the whole alignment. Which view do you think give the best 3D
superposition, and why ?
I have been having trouble with repeating 15 b, it worked the
first time. I have the FER1_SPIOL 3D structure open in JalView from
Exercise 14, and then open the FER1_MAIZE 3D structure. The first time I
did this it asked me if I wanted to overlay them, and it worked. Now,
when I try to redo the whole procedure, when I open the FER1_MAIZE
structure it just opens in a separate 3D window and doesn't prompt me
about overlaying the two 3D structures, so I am left with two separate
structures in different windows, rather than both structures overlapped
and aligned in a single 3D view window.
How do I get around this?
Thanks,
Kathleen McLeod _______________________________________________
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