In this example, we will learn to use the
building loop tools.
Step by Step
open three copies of the pdb file 1CRN provided with the
Use the Display menu to bring up the Layer Infos Window.
Hide the second and third copies of the protein.
Now use the "Build Loop" item of the "Build" menu. You
will be prompted to pick two residues which will serve as
"anchors ones". Pick L18 and A24 (the blue and the green
residues). After a while, a window appears, containing a
list of possible loops. The currently selected loop appears
clash score: 1
C-N+ CA-C-N+ C-N+-CA+
0.04 -1.48 -7.09
0.06 0.00 0.00
-0.11 0.00 0.00
-0.11 0.00 0.00
0.36 0.00 0.00
0.33 0.00 0.00
0.47 0.00 0.00
0.36 0.00 0.00
The first column gives the diviation in Å to the
ideal closure bond length, while the next two columns give
the deviation (in degrees) to the ideal angle closure. As
you can see, the first loop is the only one with the values
computed. Simply click on a line to see how well fits the
next loop. Note that you can also use the up and down arrows
keys to browse among the solutions.
To help you find the best loop, a count of the clashes
(bad contacts or H-bonds) is displayed at the top of the
window. There is also an energy information (computed with a
partial implementation of the
force-Field) that appears after the "FF" text, and a mean
force potential value (PP) computed from a "Sippl-like" mean
force potential [ref. 6].
You can click on either of those lines of the header to
sort the results accordingly to this specific criterion.
Play a little with the various loops proposed, and then
select one that seems good enough.
Now make the second copy of 1crn (the one in the second
layer) visible again and compare your best solution with the
Hide the first copy of 1crn (the one that contains the
rebuilt loop) and make the second layer active by clicking
on the second protein listed in the Layer Infosd Window.
Now use the "Scan Loop" item of the "Build" menu. As
before, you will be prompted to pick two residues which will
serve as "anchors ones". Again, pick L18 and A24 (the blue
and the green residues). After a while, a window appears,
containing a list of possible loops. The currently selected
loop appears in red.
The window content is slightly different, and gives you
the name of PDB files that contain a suitable loop, the
chain identifyer, the starting residue, the sequence of the
possible fragment, and the resolution (in Å) at which
the structure has been solved. Note that a resolution of
0.0Å means that the structure has been solved by NMR,
whereas a resolution of 9.99Å means that the source
structure is a model.
PGTPE clash score:1 bad G->X: 0
. ... (-3) bad Phi/Psi:2 bad X->P: 1
HLEHK PP:-10.46 bad X->P: 2
FF:34753.9 access:0.00 rms:0.00
2STV 10 HLEHK 2.50
2STV 92 VLNTA 2.50
1PYP 113 NNPID 3.00
4PTI 35 GCRAK 1.50
1EST 61 NQNNG 2.50
5ABP 130 KESAV 1.80
8ADH 140 GTSTF 2.40
8ADH 212 AGAAR 2.40
The header gives you the sequence of the loop you want to
build, aligned with the sequence of a fragment selected from
a database of folds. The similarity score for the fragment
appears under parenthesis and is computed from the PAM200
matrix. In addition to those informations, you have as
before, a Force Field score, a Mean Force Potential Score, a
clash score, and the number of residues from the source loop
that have bad phi/psi angles (in other words, residues that
would have phi/psi angles laying out of the allowed zones of
the ramachandran plot).
Also, you have to consider that Gly and Pro are somehow
special residues that adopt special phi/psi combinations.
Gly can accept any kind of combination, whereas Pro have phi
angles constrained around -60 degrees. Therefore, the number
of "bad" transversions (Gly in the source loop that would
not happily become something else in the loop you want to
build; or residues that would not happily become a Pro) are
also summarized in the header.
As for the previous building loop tool, you can sort the
loops by energies or clashes to ease the process of
identifying the best loop.
Select a suitable loop, and make the third layer visible
to compare with the actual solution.
Remark: After having constructed your loops, an
energy minimisation is mandatory. Swiss-PdbViewer does not
provide energy miminization facility, but can export scripts
to drive external minimisation