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NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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  #1  
Old 12-28-2005, 08:38 PM
tmc tmc is offline
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Hello,
I have some questions regarding the alignment matrix and I will be very much grateful if you could clarify my doubts.

Question 1:
1) I like to calculate the angle between the magnetic field and X,Y & Z axes of the alignment frame. For that, I have run PALES and got the values for Sxx, Sxy, Sxz, Syy & Syz. From Sxx value I have calculated cos(tx) and cos(ty) from Syy. Substituting these values in 1/2(3cos(tx)*cos(ty)), I calculated Sxy. But, this calculated value does not match with Sxy obtained from PALES.

Question 2:
I found that the saupe parameters are in the order of 10 to the power -3 & above. However, an artile about the implimentation of svd procedure (Losonczi etal., J. Magnetic Resonance, 138,334-342 (1999)) indicates that the value of S's should lie between ~-1.0 to +1.0.

Question 3:
I found in the literature that Dconst= -mu*gamma(i)*gamma(j)*h/8*pi*pi*pi*r*r*r (Zweckstetter & Ad Bax, JACS, 2000, Tsui etal, 2000, J. Bio. Mol. NMR). However, an additional 2/3 term is found in the article by Bastiaan et al., Annual reports on NMR spectroscopy, 1987.
I will be very much thanful if you could help me to understand these.

Thank you
then
Reply With Quote


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Best Answer - Posted by rank
Quote:
Originally posted by tmc@Dec 28 2005, 04:38 PM
Hello,
* I have some questions regarding the alignment matrix and I will be very much grateful if you could clarify my doubts.

Question 1:
1) I like to calculate the angle between the magnetic field and X,Y & Z axes of the alignment frame. For that, I have run PALES and got the values for Sxx, Sxy, Sxz, Syy & Syz. From Sxx value I have calculated cos(tx) and cos(ty) from Syy. Substituting these values in 1/2(3cos(tx)*cos(ty)), I calculated Sxy. But, this calculated value does not match with Sxy obtained from PALES.

When you run PALES, it should report you the magnitude of alignment, that is Sxx, Syy, Szz, etc. It should tell you the Euler angles correspondingly, right? So you can calculate the angles from these euler angles. For instance, angle between magnetic field and Szz is the Euler angle beta.

Question 2:
I found that the saupe parameters are in the order of 10 to the power -3 & above. However, an artile about the implimentation of svd procedure (Losonczi etal., J. Magnetic Resonance, 138,334-342 (1999)) indicates that the value of S's should lie between ~-1.0 to +1.0.

Hey, that is because they use different unit. It is scaled by a constant, Gamma(I)*Gamma(S)/r^3.

Question 3:
I found in the literature that Dconst= -mu*gamma(i)*gamma(j)*h/8*pi*pi*pi*r*r*r (Zweckstetter & Ad Bax, JACS, 2000, Tsui etal, 2000, J. Bio. Mol. NMR). However, an additional 2/3 term is found in the article by Bastiaan et al., Annual reports on NMR spectroscopy, 1987.
That is because they use different definition of S and R. Some guys use S and eta.

I will be very much thanful if you could help me to understand these.

Thank you
then
[snapback]131[/snapback]

  #2  
Old 08-11-2006, 07:28 PM
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Default

Quote:
Originally posted by tmc@Dec 28 2005, 04:38 PM
Hello,
* I have some questions regarding the alignment matrix and I will be very much grateful if you could clarify my doubts.

Question 1:
1) I like to calculate the angle between the magnetic field and X,Y & Z axes of the alignment frame. For that, I have run PALES and got the values for Sxx, Sxy, Sxz, Syy & Syz. From Sxx value I have calculated cos(tx) and cos(ty) from Syy. Substituting these values in 1/2(3cos(tx)*cos(ty)), I calculated Sxy. But, this calculated value does not match with Sxy obtained from PALES.

When you run PALES, it should report you the magnitude of alignment, that is Sxx, Syy, Szz, etc. It should tell you the Euler angles correspondingly, right? So you can calculate the angles from these euler angles. For instance, angle between magnetic field and Szz is the Euler angle beta.

Question 2:
I found that the saupe parameters are in the order of 10 to the power -3 & above. However, an artile about the implimentation of svd procedure (Losonczi etal., J. Magnetic Resonance, 138,334-342 (1999)) indicates that the value of S's should lie between ~-1.0 to +1.0.

Hey, that is because they use different unit. It is scaled by a constant, Gamma(I)*Gamma(S)/r^3.

Question 3:
I found in the literature that Dconst= -mu*gamma(i)*gamma(j)*h/8*pi*pi*pi*r*r*r (Zweckstetter & Ad Bax, JACS, 2000, Tsui etal, 2000, J. Bio. Mol. NMR). However, an additional 2/3 term is found in the article by Bastiaan et al., Annual reports on NMR spectroscopy, 1987.
That is because they use different definition of S and R. Some guys use S and eta.

I will be very much thanful if you could help me to understand these.

Thank you
then
[snapback]131[/snapback]
Reply With Quote


Did you find this post helpful? Yes | No
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