csdemo/talosn
An example of the TALOS-N application for
predicting protein backbone phi,psi and sidechain chi1 angles from
chemical shifts.
csdemo/spartaplus/ubiq
An example of the SPARTA+ application
for predicting protein backbone chemical shifts
from structure.
csdemo/ubiq_sa
An example of conventional structure determination with
NOE, Dipolar Couplings, J-couplings, and TALOS torsion restraints.
csdemo/dchn
An example of refining an existing structure with dipolar couplings.
csdemo/mfr
An example of the NMR homology search method called
Molecular Fragment Replacement (MFR). This example uses a combination
of dipolar couplings and chemical shifts to determine the fold
of ubiquitin, without use of NOE distance data.
TALOS Demo: Chemical Shift Database Search for Phi/Psi Angles
Simulate backbone chemical shifts from PDB structure.
View simulated vs observed chemical shifts.
cd
cd csdemo/spartaplus/ubiq
clean.com
all.com
Refinement of an Existing Structure to HN/N Dipolar Couplings
This example was kindly provided by Prof. Jaison Jacob, then
at Vanderbilt University.
In this example, an existing structure is refined against a set of HN-N
dipolar couplings. The initial structure agrees to only ~7 Hz RMSD with the
dipolar couplings, but the refined structure to better than 1 Hz RMSD.
Interestingly, the backbone of the refined structure is less than 0.3A RMSD
from the initial structure; in this case, only a small change in the
structure is needed to substantially improve the dipolar coupling agreement.
In order to use the DYNAMO structure calculation environment on a given
molecular system, we first must use the tools of DYNAMO to create tables
describing the covalent geometry of the molecules involved.
Then we must create a PDB file with a complete set of atoms in the
DYNAMO nomenclature. In this example, we start with a PDB file
produced by some other molecular analysis software. So, in the first
steps, we use the tools of DYNAMO to read the protein sequence
information from the given PDB file, and to create a complete
DYNAMO PDB file whose structure is refined to mimic the structure
in the given PDB file. Then, this DYNAMO PDB file is refined
using HN-N dipolar couplings.
The specific steps in the demonstration are:
Compute and view best-fit dipolar couplings given a PDB structure.
Create a DYNAMO structure environment based on given the PDB sequence.
Initially, the DYNAMO PDB file contains random atomic coordinates.
Refine the initial random-coordinate DYNAMO PDB file so that its
structure mimics that in the original PDB, using the heavy atom
coordinates.
Refine this structure based on HN/N dipolar couplings.
Compute and view best-fit dipolar couplings of refined structure.
Compute coordinate RMSD between original and refined structures,
and view the overlay.
cd
cd csdemo/dchn
clean.com
more all.com
all.com
(quit all graphs, quit rasmol)
Simple Conventional Structure Calculation with NOEs and Dipolar Couplings
Create a DYNAMO structure calculation environment from a protein
sequence in a shift table.
Build a helix to use as an arbitrary starting structure.
Add experimental data tables: NOEs, J-couplings, Dipolar Couplings,
TALOS torsions.
Compute a bundle of 10 structures.
Calculate and view the backbone overlay of all 10 structures.
Select the 5 best structures.
Calculate and view a backbone overlay of the best structures.
View the phi/psi trajectory of the best structures.
cd
cd csdemo/ubiq_sa
clean.com
more README
more init.com
init.com
(exit rasmol)
ls ubiq.gmc
(edit simpleSA.tcl ... change the initial random number "54321")
simpleSA.tcl
(exit rasmol)
ls ubiq.gmc
ov.tcl -r1 2 -rN 72 -ref 1ubq.pdb -in ubiq.gmc/dyn*pdb
rasmol overlay.pdb
(exit rasmol)
set goodList = (`pdbSelect.tcl -n 5 -noe 0.1 -pdb ubiq.gmc/dyn*pdb`)
ov.tcl -r1 2 -rN 72 -ref 1ubq.pdb -in $goodList
rasmol overlay.pdb
scrollRama.tcl -pdb 1ubq.pdb $goodList
Molecular Fragment Replacement
Directory: pipe/demo/mfr
The MFR method determines elements of protein structure by finding
small fragments (5-15 residues) in the PDB database whose simulated
dipolar couplings and shifts match those measured for the target
protein. These small homologous fragments can then be used in various ways
to reconstitute larger elements of protein structure.
This demo uses several types of dipolar couplings measured in two
alignment media, which allows fragments to be assembled into larger
structures of 10-50 residues or more.
The steps in this demo are:
Create a DYNAMO structure calculation environment from a
protein sequence in a shift table.
Build a helix from the given sequence.
Conduct the MFR search using dipolar couplings and backbone shifts,
excluding ubiquitin.
View the tensor magnitude with respect to residue (is tensor
uniform for whole molecule?).
Form an initial "pretzel" structure from averaged MFR angles.
View Phi/Psi trajectories for MFR results compared to known structure.
cd
cd csdemo/mfr
clean.com
ls
more README
more dObsA.tab
more ext.com
ext.com
(exit rasmol)
mfr.tcl -excl 1ubq -csThresh 2.5
more mfr.tab
plotTab.tcl -in mfr.tab -x A_DA -y A_DR
plotTab.tcl -in mfr.tab -x D_RES1 -y A_DA B_DA -yMax 0.0
mfr2init.tcl
rasmol init.pdb
scrollRama.tcl -pdb ref.pdb init.pdb -mfr mfr.tab
