NESG Wiki - User contributions [en]

CARA vs Xeasy

2017-11-06T19:47:38Z

Pwils3:

Below is concise list of key features of CARA as compared to [[XEASY]] that should help new users make a transition.

==== Data Organization ====

[[XEASY]] keeps data stored in separate files: spectra, sequence lists, atom lists, and peaklists.

CARA stores all data in a "repository" - an XML file, which contains all information (residue type definitions, spectrum types definitions, spin systems, spins, peak lists, extension scripts, paths to NMR spectra, etc.). This file typically has a .cara extension. A repository is built from a template by adding "projects". This approach allows much better control and overview over a structure project and makes sharing data among researchers easier.

Though CARA protects repositories from modifications, which may compromise its stability, repositories can be edited with a plain text or XML editor.

==== Atom Nomenclature ====

Current repository templates are designed to be compatible with the BMRB format. That is, H is used instead of HN, and glycines have HA2/3 instead of HA1/2. This is also the default format of '''cyana.lib '''in [[CYANA]] 2.1.

In addition to that, pseudoatoms are labeled as H* instead of Q* and QQ*. For example, HB is used for QB, HD1/2 for QD1/2, and HD for QQD of Leu. This is compatible with the '''pseudo=2''' setting in [[CYANA]] 2.1

==== Residues and Spin Systems ====

XEASY stores information about spin systems (also referred to as fragments in XEASY manual) and residues in the same *.seq file, and requires somewhat confusing swapping of mapping and fragment numbers for sequence-specific assignment.

CARA clearly distinguishes residues and spin systems as separate classes in repository database. Spin systems can be numbered from 1 upward. They can be linked into fragments by setting successor and predecessor tags. Fragments can be "mapped" to the sequence to see if they match a particular stretch of residues. A spin system becomes assigned when its assignment tag is set, pointing to a certain residue in the sequence.

==== Atoms and Spins ====

What XEASY refers to as atoms are called "spins" in CARA. "Atoms" in CARA form a different data class - it is a member of "residue type" as a part of molecular structure. The database of spins can be exported as an XEASY atom list, and an XEASY atom list can be imported into CARA (provided that the nomenclature matches).

While you may need to use separate atom lists with different spectra and peak lists in XEASY, CARA works with a single set of spins. Spin aliases are used in situations where the same spin has different chemical shifts (see below).

==== Spin Labels ====

Spin labels have the form [?|!]SPINLABEL[+|-x], where SPINLABEL is an alphanumeric string and +x or -x is the "offset". The question mark ? as the first character marks temporary assignments, the exclamation sign "!" - stereospecific assignments. Since + and - characters are reserved to specify offsets, lowercase letters "p" and "m" should be used instead for spin labels in GFT spectra. For example, sequential CA+CB peak should be labeled CApCB-1.

Offset designations in CARA carry more information than in XEASY - they are used to search for sequential neighbors.

==== Peak Inference and Peak Lists ====

Though peak lists in XEASY format can be exported from any spectrum, they only need to be generated for NOESY spectra to provide input to programs like CYANA and AutoStructure. They are not needed for backbone and side-chain assignment.

Peak marks, which you see in spectrum display tools ( "scopes", in this case other than MonoScope ) are displayed at positions, inferred from chemical shifts, and residue type and spectrum type definitions. Spectrum type definitions describe the correlations prouced in a given spectrum and valid spin labels in every dimension. This is equivalent to XEASY peaklists being generated from an atom list on-the-fly. If a peak is moved in CARA, then the chemical shifts of the spins involved are updated instantly. If a new peak is picked, new spins are created. These changes are synchronized across all "scopes".

==== Spectral Folding and Aliasing ====

In CARA all spins and peaks have their exact assignments and positions (in ppm). There are no folding attributes for peaks, as in XEASY. Instead, it is possible to navigate beyond the spectrum edge to display the true unfolded location.

==== Spin Links ====

Spin links do not have a direct equivalent in XEASY. They are designed to describe correlations observed in NOESY spectra, but CARA does not prescribed a unique use for them. Spin links present a good means of visualizing UPLs or short distances in NOESY spectra. Spin links can also be used instead of peak list in manual NOE assignment.

A useful feature is that a single spin link produces two peaks - the direct and transposed. Spin links and inferred peaks can be exported as XEASY peak lists.

==== Spin Aliases ====

There may be significant mismatches between related NMR spectra. Typical causes are different sample and experimental conditions, such as temperature differences or non-resonant effects, or systematic offsets, such as those between TROSY and conventional NMR spectra. In such cases spin aliases can be helpful.

The spin alias object is a child of spin. It has its own chemical shift (typically different from that of spin itself), and a tag with the ID of the spectrum, where this alias was set. Spin aliases have a purely cosmetic effect on spectral appearance, defining positions, where planes and and slices will be taken.

JOMAD Jeans If you are looking for the best [https://www.jomadjeans.com designer jeans for women], look no further than [http://jomadjeansdesignerjeansforwomen.wikidot.com JOMAD Jeans]; located in NYC. We offer fits and styles matching whatever season you find yourself in. VAGABOUND - a high waist or midrise jean with optional distressed or ripped elements. You can get skinny ankle or even a zipped ankle on these Jeans. We also have our DRIFTER model. These are athletic fit jeans- and simply the best fitting for women. These designer premium stretch denim provide unrivaled comfort and slim fit on these jeans. The color variety is amazing as well; Interested in destroyed skinny jeans? Check. High waisted flare jeans? Check. Designer ankle grazer jeans? Of course. We have all the designer inventory if you ever choose to buy jeans. If you are vertically challenged, we have jeans for short women. If you are taller, look no further than our long, high waisted fits. Our rebound denim is among the most comfortable and provides women with the best fitting jeans. They have a [https://www.jomadjeans.com skinny fit jean], and the denim fits slim and snug. We are located in New York City, but don't Hesitate to visit our store online.

We wander because we wonder. We are constantly on the move, feeding a curiosity about the world that can’t be tamed. We are classy, yet cool. Modest, yet modern. Our style is as dynamic as our lifestyle.
Inspired by the nomadic lifestyle of our ancestors, [https://rustednail56.wixsite.com/jomadjeans JOMAD Jeans] was created as a brand for people who want to live freely. Nothing–especially not clothing– should hold us back from the journey that lies ahead.

The '''Gypsy''' is a mid-rise skinny ankle jean crafted from ultimate rebound denim. Slimming fit while giving you the vintage attitude. Five-pocket styling with a zip fly and button closure

The '''Drifter''' is a high-rise kickboot jean that fits like a skinny jean through the hip and knee and then breaks into a subtle kickboot at the hem. Crafted from a ultimate stretch denim with holding power

JOMAD Jeans is located in NYC. Please utilize the below links to navigate the interior of our website.

[https://www.jomadjeans.com/collections/all JOMAD Jeans Collections] View All Collections of Jeans

[https://www.jomadjeans.com/pages/the-style-guide JOMAD Jeans Style] View our Style Guide
[https://www.jomadjeans.com/pages/about JOMAD Jeans About] About Us

[https://www.jomadjeans.com/pages/contact JOMAD Jeans Contact] Contact Us

We wander because we wonder. We are constantly on the move, feeding a curiosity about the world that can’t be tamed. We are classy, yet cool. Modest, yet modern. Our style is as dynamic as our lifestyle.
Inspired by the nomadic lifestyle of our ancestors, JOMAD was created as a brand for people who want to live freely. Nothing–especially not clothing– should hold us back from the journey that lies ahead.

Jomad Jeans: Skinny Straight Jeans | High Rise Flare Jeans | Stretch Rebound Denim | Buy Best Fitting Jeans for Women | Athletic Fit | Slim Fit | Ankle Grazer Jeans | Mid Rise

It is recommended to have all spectra calibrated and matched as best as possible, before resorting to spin aliases. Also you would want to have the main chemical shifts set to match the NOESY spectra, since they are exported for use in automated structure calculation, and use aliases for other spectra, such as HCCH-COSY.

==== Scripting ====

CARA functionality is extended by scripts in Lua programming language ([http://www.lua.org/ www.lua.org]). Besides default Lua functionality interface to many CARA functions is available.

-- AlexEletski - 06 Mar 2007

[[Category:CARA]][[Category:Resonance_Assignment]][[Category:XEasy]]

Aromatic side chain assignment with Aro-HCCH-COSY in XEASY

2017-11-06T19:46:32Z

Pwils3:

Aromatic (4,3)D HCCH shows signals for aromatic H-C-C-H moeties. See [[Side chain assignment with aliphatic (4,3)D HCCH-COSY in XEASY|aliphatic (4,3)D HCCH Analysis]] for comparison.

Before proceeding, it is helpful to look for the QD (Phe and Tyr), HD2 (His), and HD1 (Trp) resonances in the simultaneous [1H, 1H]-NOESY. Look for a consistent peak that is visible in the amide, alpha, and beta strips near 7ppm.

'''Phe, Tyr, and His'''

*Run the following macro in UBNMR to generate a peaklist and atom list: 
<pre> init
read seq myprot.seq #change filename to something appropriate
read prot noe.prot #change filename to your most current prot list

add GFTatom COSY_C ATTACHED_H

simulate 3D CG COSY_H 0 1
simulate 3D CG COSY_C 0 1
simulate 3D CG1 COSY_CH 0 1
simulate 3D CG1 COSY_C 0 1
simulate 3D CG2 COSY_CH 0 1
simulate 3D CG2 COSY_C 0 1

simulate 3D CD COSY_CH 0 2
simulate 3D CD COSY_C 0 2
simulate 3D CD1 COSY_CH 0 2
simulate 3D CD1 COSY_C 0 2
simulate 3D CD2 COSY_CH 0 2
simulate 3D CD2 COSY_C 0 2

simulate 3D CZ2 COSY_CH 0 3
simulate 3D CZ2 COSY_C 0 3
simulate 3D CZ3 COSY_CH 0 3
simulate 3D CZ3 COSY_C 0 3
simulate 3D CE3 COSY_CH 0 4
simulate 3D CE3 COSY_C 0 4
simulate 3D CH2 COSY_CH 0 4
simulate 3D CH2 COSY_C 0 4

write prot hcchAroI1.prot #the newly created starting prot list
write peaks hcchAroI1.peaks #the newly created starting peak list
</pre>
*In XEASY, use <tt>ns</tt> to load the three sub-spectra of aromatic (4,3)D HCCH; use <tt>ls</tt>, <tt>lp</tt> and <tt>lc</tt> to load the sequence, peak list, and chemical shift list, respectively and <tt>se</tt>, <tt>gs</tt> to sort and display [w1(13C;1H);w3(1H)]-strips.
*In XEASY, use <tt>pm</tt>, <tt>es</tt>, <tt>se</tt> and <tt>gs</tt> (or <tt>sf</tt>) to display [w1(13C;1H);w2(13C)]-planes, and sort and [w1(13C;1H);w2(13CD)]-planes; use <tt>mr</tt> to accurately adjust peak positions to assign 13CD chemical shifts
*use <tt>pm</tt> and <tt>gs</tt> to re-display [w1(13C;1H); w3(1H)]-planes and [w1(13C;1H); w3(1H)]-strips; use <tt>mr</tt> to accurately adjust peak positions to confirm QD chemical shifts. The strips in the basic spectra are expected to exhibit peaks at 13CD, 13Main.CE, ..., 13CD±QD and 13CD±QE. Use <tt>mr</tt> to accurately position peaks along w1; use <tt>ac</tt>, <tt>wp</tt> and <tt>wc</tt> to save updated PeakList and AtomList.

JOMAD Jeans If you are looking for the best [https://www.jomadjeans.com designer jeans for women], look no further than [http://jomadjeansdesignerjeansforwomen.wikidot.com JOMAD Jeans]; located in NYC. We offer fits and styles matching whatever season you find yourself in. VAGABOUND - a high waist or midrise jean with optional distressed or ripped elements. You can get skinny ankle or even a zipped ankle on these Jeans. We also have our DRIFTER model. These are athletic fit jeans- and simply the best fitting for women. These designer premium stretch denim provide unrivaled comfort and slim fit on these jeans. The color variety is amazing as well; Interested in destroyed skinny jeans? Check. High waisted flare jeans? Check. Designer ankle grazer jeans? Of course. We have all the designer inventory if you ever choose to buy jeans. If you are vertically challenged, we have jeans for short women. If you are taller, look no further than our long, high waisted fits. Our rebound denim is among the most comfortable and provides women with the best fitting jeans. They have a [https://www.jomadjeans.com skinny fit jean], and the denim fits slim and snug. We are located in New York City, but don't Hesitate to visit our store online.

We wander because we wonder. We are constantly on the move, feeding a curiosity about the world that can’t be tamed. We are classy, yet cool. Modest, yet modern. Our style is as dynamic as our lifestyle.
Inspired by the nomadic lifestyle of our ancestors, [https://rustednail56.wixsite.com/jomadjeans JOMAD Jeans] was created as a brand for people who want to live freely. Nothing–especially not clothing– should hold us back from the journey that lies ahead.

The '''Gypsy''' is a mid-rise skinny ankle jean crafted from ultimate rebound denim. Slimming fit while giving you the vintage attitude. Five-pocket styling with a zip fly and button closure

The '''Drifter''' is a high-rise kickboot jean that fits like a skinny jean through the hip and knee and then breaks into a subtle kickboot at the hem. Crafted from a ultimate stretch denim with holding power

JOMAD Jeans is located in NYC. Please utilize the below links to navigate the interior of our website.

[https://www.jomadjeans.com/collections/all JOMAD Jeans Collections] View All Collections of Jeans

[https://www.jomadjeans.com/pages/the-style-guide JOMAD Jeans Style] View our Style Guide
[https://www.jomadjeans.com/pages/about JOMAD Jeans About] About Us

[https://www.jomadjeans.com/pages/contact JOMAD Jeans Contact] Contact Us

We wander because we wonder. We are constantly on the move, feeding a curiosity about the world that can’t be tamed. We are classy, yet cool. Modest, yet modern. Our style is as dynamic as our lifestyle.
Inspired by the nomadic lifestyle of our ancestors, JOMAD was created as a brand for people who want to live freely. Nothing–especially not clothing– should hold us back from the journey that lies ahead.

Jomad Jeans: Skinny Straight Jeans | High Rise Flare Jeans | Stretch Rebound Denim | Buy Best Fitting Jeans for Women | Athletic Fit | Slim Fit | Ankle Grazer Jeans | Mid Rise

*In UBNMR, run <tt>updatacosyGFT</tt> to calculate SQ shifts from updated AtomList. Repeat the above steps for the QE<tt>strips</tt> and assign QE. Note that for His, the assignment is often complicated by the presence of strong signals from the His-tag introduced to facilitate protein purification. The QE strip in the basic spectra is expected to exhibit peaks at 13CD, 13Main.CE, 13CZ, ..., 13CD±QD, 13Main.CE±QE and possibly 13CZ±1HZ (for Phe only).

'''TRP'''

*In XEASY, repeat steps 1-3 for strips in the order HH2 > HZ2 > HZ3 > HE3 (instead of the strip order QD > QE for Tyr and Phe). In HH2-strips, assign 13CH2±1HH2, and 13CZ2±1HZ2. In HZ2-strips assign 13CZ2± 1HH2, 13CZ2±1HZ2 and 13CZ3±1HZ3. In HZ3-strips, assign 13CZ3±1HZ3, 13CZ2±1HZ2 and 13CZ3±1HZ3. In HZ3 strip, assign 13CZ3±1HZ3, and 13CE3±1HE3.

Routine Processing Procedure for 3D 15N and 13C-edited Experiments

2017-11-06T19:42:48Z

Pwils3:

'''NMR Data Processing > Routine 3D Experiments via NMRPipe'''
<div> </div>
===== Brief Description =====

The procedure for processing a 3D dataset is fairly similar to the ones described for the 2D dataset along with additional parameters for a third dimension (generally refered to as the z dimension). For nD dataset where the indirect dimension(s) is collected with few points, it is often advantageous to increase the number of points and digital resolution using ‘Linear Prediction’. This calculation determines the frequency and decay rate of the peaks in an FID or interferrogram, and extends them mathematically. It is very useful for 15N and 13C-edited 3D dataset where experimental time is needed to improve S/N, so the number of increments is limited. It is important to mention that ‘Linear Prediction’ on the selected dimension of a 3D dataset is performed after the other two dimensions have been processed. An example processing script for HNCO experiment is shown here, where the HN dimension (x) and N dimension (z) are first processed followed by the linear prediction and processing of the CO dimension (y). The N dimension is then inverse transformed, linear predicted, and retransformed. This processing script is also applicable to the majority of 3D 15N and 13C-edited datasets for protein related work.

===== Software Information =====

NMRPipe (download information and user manual) [http://spin.niddk.nih.gov/NMRPipe/ http://spin.niddk.nih.gov/NMRPipe/] Brief descriptions of specific functions are accessible via nmrPipe –

:‘nmrPipe –help’ will list most functions.
:‘nmrPipe –fn GM –help’ will give description of the GM function.

 Supported Platforms

:Linux (RedHat Linux/Fedora)
:Mac OS X (10.3.4 and up)
:SGI Irix  (6.2 and up)
:Sparc Solaris (2 and up)
:Windows XP Pro with Microsoft Services for UNIX (SFU 3.5)

===== Converting Spectrometer Data into NMRPipe Format =====

The conversion of data from spectrometer format to NMRPipe format is usually done using a build-in program called ‘varian’ for Varian a dataset ('bruker' for a Bruker dataset and 'delta' for dataset from JEOL). [[Brief description of philosophy, commands, and functions of NMRPipe|Brief summaries of the build-in program can be found here]]. 

 

Step 1: Under the same directory where the procpar and fid files are, type ‘varian’ and this will start a tcl/tk script that brings up two windows.

[[Image:Varian-utility-raw.png]] [[Image:Varian-script-raw.png]] 

Step 2: Click on the ‘Read Parameters’ button and the script will read the parameter file (‘procpar’) and update the parameters.

[[Image:Varian-utility-3D.png]] [[Image:Varian-script-3D.png]] 

The template shows parameters for three dimensions x, y, and z for HN, CO, and N, respectively. More detailed description of the input script can be found at routine 2D experiment or NMRPipe user manual.

:‘-aqORD 1’ !!! Varian dataset when ‘array=phase,phase2’
:‘-xMODE complex’ !!! For the direct dimension
:‘-yMODE: complex’ !!! For the CO dimension
:‘-zMODE: Rance-Kay’ !!! For sensitivity enhanced experiment

 

Step 3: Click on ‘Save Script’, and then ‘Execute Script’. The converted planes in NMRPipe format will be stored in the ‘data’ directory along with an UNIX shell script called ‘fid.com’. 

===== Processing and Visualizing 3D Dataset =====

For information on the macro editor of nmrDraw, see [[Routine 2D Experiment|routine processing procedure for 2D experiment]]. An example of processing script for a 3D HNCO spectrum with linear prediction in the y and z dimensions is shown below.
<pre>!!! Part 1, process the directly-detected x-axis !!!
xyz2pipe -in fid/test%03d.fid -x -verb \
| nmrPipe -fn SOL \ ## Removed residual solvent
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \ ## Apodization
| nmrPipe -fn ZF -auto \ ## Zero fill
| nmrPipe -fn FT \ ## Fourier transformation
| nmrPipe -fn PS -p0 43 -p1 0.0 -di \ ## Phase correction
| nmrPipe -fn EXT -left -sw \ ## Extract left half spectrum
| pipe2xyz -out lp/test%03d.ft3 -x

!!! Part 2, process the indirectly-detected z-axis !!!
xyz2pipe -in lp/test%03d.ft3 -z -verb \
| nmrPipe -fn SP -off 0.5 -end 0.95 -pow 1 -c 0.5 \ ## Apodization
| nmrPipe -fn ZF -auto \ ## Zero fill
| nmrPipe -fn FT \ ## Fourier transformation
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di \ ## Phase correction
| pipe2xyz -out lp/test%03d.ft3 -z –inPlace

!!! predict and process the indirect-detected y-axis !!!
xyz2pipe -in lp/test%03d.ft3 -y -verb \
| nmrPipe -fn LP -fb -ord 10 \ ## Linear Prediction
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 1.0 \ ## Apodization
| nmrPipe -fn ZF -auto \ ## Zero fill
| nmrPipe -fn FT \ ## Fourier transformation
| nmrPipe -fn PS -p0 -135 -p1 180 -di \ # Phase correction
| pipe2xyz -out lp/test%03d.ft3 -y -inPlace

!!! inverse, predict, and re-process the z-axis
xyz2pipe -in lp/test%03d.ft3 -z -verb \
| nmrPipe -fn HT -auto \
| nmrPipe -fn PS -inv -hdr \
| nmrPipe -fn FT -inv \
| nmrPipe -fn ZF -inv \
| nmrPipe -fn SP -inv -hdr \
| nmrPipe -fn LP -fb \ ## Linear prediction
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \ ## Apodization
| nmrPipe -fn ZF -auto \ ## Zero fill
| nmrPipe -fn FT \ ## Fourier transformation
| nmrPipe -fn PS -hdr -di \
| pipe2xyz -out lp/test%03d.ft3 -z -inPlace
</pre>
===== Suggested Workflow =====

:Step 1: Generate the processing script with the appropriate commands and functions using the macro editor or modified existing script. Set both the p0 and p1 phasing values of the direct dimension to 0.
:Step 2: Execute the processing script in a UNIX terminal.  The 2D projection planes of the 3D dataset can be created using the build-in program readROI for phase correction  (execute the following command in a UNIX terminal, ‘nmrWish –f [[Media:Project.txt|Project.txt]]’).  Load the projection plane into nmrDraw to perform phase correction and optimize the applied functions. A 1D horizontal trace can be activate by typing ‘h’ in the spectrum window and the phase of the dimension can be adjusted using the P0 and P1 slider bars. To phase an indirect dimension, type 'v'.  Now the P0 and P1 slider bars will change the phase of the indirectly detected dimension.
:Step 3: Execute the processing script with optimized parameters.
:Step 4: Convert the processed data to the format of graphical NMR assignment program.

 Updated by Hsiau-Wei Lee, 2011

JOMAD Jeans If you are looking for the best [https://www.jomadjeans.com designer jeans for women], look no further than [http://jomadjeansdesignerjeansforwomen.wikidot.com JOMAD Jeans]; located in NYC. We offer fits and styles matching whatever season you find yourself in. VAGABOUND - a high waist or midrise jean with optional distressed or ripped elements. You can get skinny ankle or even a zipped ankle on these Jeans. We also have our DRIFTER model. These are athletic fit jeans- and simply the best fitting for women. These designer premium stretch denim provide unrivaled comfort and slim fit on these jeans. The color variety is amazing as well; Interested in destroyed skinny jeans? Check. High waisted flare jeans? Check. Designer ankle grazer jeans? Of course. We have all the designer inventory if you ever choose to buy jeans. If you are vertically challenged, we have jeans for short women. If you are taller, look no further than our long, high waisted fits. Our rebound denim is among the most comfortable and provides women with the best fitting jeans. They have a [https://www.jomadjeans.com skinny fit jean], and the denim fits slim and snug. We are located in New York City, but don't Hesitate to visit our store online.

We wander because we wonder. We are constantly on the move, feeding a curiosity about the world that can’t be tamed. We are classy, yet cool. Modest, yet modern. Our style is as dynamic as our lifestyle.
Inspired by the nomadic lifestyle of our ancestors, [https://rustednail56.wixsite.com/jomadjeans JOMAD Jeans] was created as a brand for people who want to live freely. Nothing–especially not clothing– should hold us back from the journey that lies ahead.

The '''Gypsy''' is a mid-rise skinny ankle jean crafted from ultimate rebound denim. Slimming fit while giving you the vintage attitude. Five-pocket styling with a zip fly and button closure

The '''Drifter''' is a high-rise kickboot jean that fits like a skinny jean through the hip and knee and then breaks into a subtle kickboot at the hem. Crafted from a ultimate stretch denim with holding power

JOMAD Jeans is located in NYC. Please utilize the below links to navigate the interior of our website.

[https://www.jomadjeans.com/collections/all JOMAD Jeans Collections] View All Collections of Jeans

[https://www.jomadjeans.com/pages/the-style-guide JOMAD Jeans Style] View our Style Guide

Routine Processing Procedure for 3D 15N and 13C-edited Experiments

2017-11-06T19:41:22Z

Pwils3:

'''NMR Data Processing > Routine 3D Experiments via NMRPipe'''
<div> </div>
===== Brief Description =====

The procedure for processing a 3D dataset is fairly similar to the ones described for the 2D dataset along with additional parameters for a third dimension (generally refered to as the z dimension). For nD dataset where the indirect dimension(s) is collected with few points, it is often advantageous to increase the number of points and digital resolution using ‘Linear Prediction’. This calculation determines the frequency and decay rate of the peaks in an FID or interferrogram, and extends them mathematically. It is very useful for 15N and 13C-edited 3D dataset where experimental time is needed to improve S/N, so the number of increments is limited. It is important to mention that ‘Linear Prediction’ on the selected dimension of a 3D dataset is performed after the other two dimensions have been processed. An example processing script for HNCO experiment is shown here, where the HN dimension (x) and N dimension (z) are first processed followed by the linear prediction and processing of the CO dimension (y). The N dimension is then inverse transformed, linear predicted, and retransformed. This processing script is also applicable to the majority of 3D 15N and 13C-edited datasets for protein related work.

===== Software Information =====

NMRPipe (download information and user manual) [http://spin.niddk.nih.gov/NMRPipe/ http://spin.niddk.nih.gov/NMRPipe/] Brief descriptions of specific functions are accessible via nmrPipe –

:‘nmrPipe –help’ will list most functions.
:‘nmrPipe –fn GM –help’ will give description of the GM function.

 Supported Platforms

:Linux (RedHat Linux/Fedora)
:Mac OS X (10.3.4 and up)
:SGI Irix  (6.2 and up)
:Sparc Solaris (2 and up)
:Windows XP Pro with Microsoft Services for UNIX (SFU 3.5)

===== Converting Spectrometer Data into NMRPipe Format =====

The conversion of data from spectrometer format to NMRPipe format is usually done using a build-in program called ‘varian’ for Varian a dataset ('bruker' for a Bruker dataset and 'delta' for dataset from JEOL). [[Brief description of philosophy, commands, and functions of NMRPipe|Brief summaries of the build-in program can be found here]]. 

 

Step 1: Under the same directory where the procpar and fid files are, type ‘varian’ and this will start a tcl/tk script that brings up two windows.

[[Image:Varian-utility-raw.png]] [[Image:Varian-script-raw.png]] 

Step 2: Click on the ‘Read Parameters’ button and the script will read the parameter file (‘procpar’) and update the parameters.

[[Image:Varian-utility-3D.png]] [[Image:Varian-script-3D.png]] 

The template shows parameters for three dimensions x, y, and z for HN, CO, and N, respectively. More detailed description of the input script can be found at routine 2D experiment or NMRPipe user manual.

:‘-aqORD 1’ !!! Varian dataset when ‘array=phase,phase2’
:‘-xMODE complex’ !!! For the direct dimension
:‘-yMODE: complex’ !!! For the CO dimension
:‘-zMODE: Rance-Kay’ !!! For sensitivity enhanced experiment

 

Step 3: Click on ‘Save Script’, and then ‘Execute Script’. The converted planes in NMRPipe format will be stored in the ‘data’ directory along with an UNIX shell script called ‘fid.com’. 

===== Processing and Visualizing 3D Dataset =====

For information on the macro editor of nmrDraw, see [[Routine 2D Experiment|routine processing procedure for 2D experiment]]. An example of processing script for a 3D HNCO spectrum with linear prediction in the y and z dimensions is shown below.
<pre>!!! Part 1, process the directly-detected x-axis !!!
xyz2pipe -in fid/test%03d.fid -x -verb \
| nmrPipe -fn SOL \ ## Removed residual solvent
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \ ## Apodization
| nmrPipe -fn ZF -auto \ ## Zero fill
| nmrPipe -fn FT \ ## Fourier transformation
| nmrPipe -fn PS -p0 43 -p1 0.0 -di \ ## Phase correction
| nmrPipe -fn EXT -left -sw \ ## Extract left half spectrum
| pipe2xyz -out lp/test%03d.ft3 -x

!!! Part 2, process the indirectly-detected z-axis !!!
xyz2pipe -in lp/test%03d.ft3 -z -verb \
| nmrPipe -fn SP -off 0.5 -end 0.95 -pow 1 -c 0.5 \ ## Apodization
| nmrPipe -fn ZF -auto \ ## Zero fill
| nmrPipe -fn FT \ ## Fourier transformation
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di \ ## Phase correction
| pipe2xyz -out lp/test%03d.ft3 -z –inPlace

!!! predict and process the indirect-detected y-axis !!!
xyz2pipe -in lp/test%03d.ft3 -y -verb \
| nmrPipe -fn LP -fb -ord 10 \ ## Linear Prediction
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 1.0 \ ## Apodization
| nmrPipe -fn ZF -auto \ ## Zero fill
| nmrPipe -fn FT \ ## Fourier transformation
| nmrPipe -fn PS -p0 -135 -p1 180 -di \ # Phase correction
| pipe2xyz -out lp/test%03d.ft3 -y -inPlace

!!! inverse, predict, and re-process the z-axis
xyz2pipe -in lp/test%03d.ft3 -z -verb \
| nmrPipe -fn HT -auto \
| nmrPipe -fn PS -inv -hdr \
| nmrPipe -fn FT -inv \
| nmrPipe -fn ZF -inv \
| nmrPipe -fn SP -inv -hdr \
| nmrPipe -fn LP -fb \ ## Linear prediction
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \ ## Apodization
| nmrPipe -fn ZF -auto \ ## Zero fill
| nmrPipe -fn FT \ ## Fourier transformation
| nmrPipe -fn PS -hdr -di \
| pipe2xyz -out lp/test%03d.ft3 -z -inPlace
</pre>
===== Suggested Workflow =====

:Step 1: Generate the processing script with the appropriate commands and functions using the macro editor or modified existing script. Set both the p0 and p1 phasing values of the direct dimension to 0.
:Step 2: Execute the processing script in a UNIX terminal.  The 2D projection planes of the 3D dataset can be created using the build-in program readROI for phase correction  (execute the following command in a UNIX terminal, ‘nmrWish –f [[Media:Project.txt|Project.txt]]’).  Load the projection plane into nmrDraw to perform phase correction and optimize the applied functions. A 1D horizontal trace can be activate by typing ‘h’ in the spectrum window and the phase of the dimension can be adjusted using the P0 and P1 slider bars. To phase an indirect dimension, type 'v'.  Now the P0 and P1 slider bars will change the phase of the indirectly detected dimension.
:Step 3: Execute the processing script with optimized parameters.
:Step 4: Convert the processed data to the format of graphical NMR assignment program.

 Updated by Hsiau-Wei Lee, 2011

JOMAD Jeans If you are looking for the best [https://www.jomadjeans.com designer jeans for women], look no further than [http://jomadjeansdesignerjeansforwomen.wikidot.com JOMAD Jeans]; located in NYC. We offer fits and styles matching whatever season you find yourself in. VAGABOUND - a high waist or midrise jean with optional distressed or ripped elements. You can get skinny ankle or even a zipped ankle on these Jeans. We also have our DRIFTER model. These are athletic fit jeans- and simply the best fitting for women. These designer premium stretch denim provide unrivaled comfort and slim fit on these jeans. The color variety is amazing as well; Interested in destroyed skinny jeans? Check. High waisted flare jeans? Check. Designer ankle grazer jeans? Of course. We have all the designer inventory if you ever choose to buy jeans. If you are vertically challenged, we have jeans for short women. If you are taller, look no further than our long, high waisted fits. Our rebound denim is among the most comfortable and provides women with the best fitting jeans. They have a [https://www.jomadjeans.com skinny fit jean], and the denim fits slim and snug. We are located in New York City, but don't Hesitate to visit our store online.

We wander because we wonder. We are constantly on the move, feeding a curiosity about the world that can’t be tamed. We are classy, yet cool. Modest, yet modern. Our style is as dynamic as our lifestyle.
Inspired by the nomadic lifestyle of our ancestors, [https://rustednail56.wixsite.com/jomadjeans
JOMAD Jeans] was created as a brand for people who want to live freely. Nothing–especially not clothing– should hold us back from the journey that lies ahead.

The '''Gypsy''' is a mid-rise skinny ankle jean crafted from ultimate rebound denim. Slimming fit while giving you the vintage attitude. Five-pocket styling with a zip fly and button closure

The '''Drifter''' is a high-rise kickboot jean that fits like a skinny jean through the hip and knee and then breaks into a subtle kickboot at the hem. Crafted from a ultimate stretch denim with holding power

http://wallinside.com/post-61342343-finding-listed-in-search-engines.html
http://www.dailystrength.org/journals/affordable-search-engine-optimization-described-1

JOMAD Jeans is located in NYC. Please utilize the below links to navigate the interior of our website.

[https://www.jomadjeans.com/collections/all JOMAD Jeans Collections] View All Collections of Jeans

[https://www.jomadjeans.com/pages/the-style-guide JOMAD Jeans Style] View our Style Guide

Talk:Main Page

2017-11-06T19:31:14Z

Pwils3: Created page with '__NOTOC__ <big>'''Welcome to the NESG Wiki!'''</big> The NESG Wiki is a medium for sharing experimental protocols as well as training an educational materials in the fiel…'

Main Page

2017-11-06T19:28:43Z

Pwils3:

__NOTOC__

<big>'''Welcome to the NESG Wiki!'''</big> 

The NESG Wiki is a medium for sharing experimental protocols as well as training an educational materials in the fields of structural biology, structural genomics and biomolecular NMR.

Please check out [[NESG NMR wiki workshop at the 2010 Keystone meeting|NESG NMR wiki workshop presentations at the 2010 Keystone meeting]]

== Protein Sample Production ==

{| cellspacing="1" class="FCK__ShowTableBorders"
|- valign="top"
|
*[https://jomadjeans.wordpress.com/ Target] selection|NESG target selection 
*[[DNA cloning protocols|DNA cloning protocols]] 
*[https://www.quora.com/unanswered/How-comfortable-are-JOMAD-Jeans Pro]tein purification|Protein expression and purification protocols  
*Sample Optimization
**[[Construct optimization]]
**[[Buffer optimization]]
**[[Cofactor optimization]]

|
*Protein Sample Analysis
**[[SDS page gel]]
**[[Protein concentration|Protein concentration measurements]]
**[[Oligomerization Status|Assessment of Oligomerization State]]
***[[Gel filtration and light scattering|gel-filtration and light scattering]]
***[[NMR determined Rotational correlation time]]
**[[MassSpectrometry|Mass spectrum]]
**[[NMR screening]]

 

|}

== NMR Data Acquisition ==

{| class="FCK__ShowTableBorders" cellspacing="1"
|- valign="top"
|
*Routine operation
**[[NMR Sample Preparation]]
**[[Inserting NMR Sample]]
**[[Tuning and matching]]
**[[Deuterium Lock]]
**[[Shimming]]
**[[Pulse width calibration]]
**[[Temperature calibration]]
**[[Chemical shift referencing]]
*Advanced operation
**[[Deuterium pulse width calibration and decoupling]]

|
*NMR data acquisition for protein structure determination
**[[Common NMR experiment sets]]
**[[NMR experiment setup scripts for VNMRJ|Custom NMR experiment setup scripts for VNMRJ]]
**[[Estimation of rotational correlation time]]
**[https://www.jomadjeans.com High waisted flare jeans]
**[[Simultaneous 13C,15N-resolved NOESY]]
**[[2D (13C, 1H) HSQC for fractionally 13C-labeled samples|2D [13C, 1H]-HSQC for fractionally 13C-labeled samples]]
**[https://www.jomadjeans.com Ankle grazer jeans]
*[[Setting up non-uniformly sampled spectra|Non-uniform sampling (NUS) ]]
**[https://www.jomadjeans.com designer jeans for women]
**[[Setting up non-uniformly sampled spectra/NUS guide for Bruker according to Arrowsmith group in Toronto|NUS - Bruker]]

|
*Maintenance (VARIAN)
**[[Installing and updating BioPack]]
**[http://prime.ece.mtu.edu/wiki/index.php?title=User:Jomadjeans Full probefile calibration]
**[http://jomadjeansnyc.wikidot.com/ Reboot]ing spectrometer console
**[http://jomadjeansdesignerjeansforwomen.wikidot.com Conditioning procedure for cryogenic probes]

|}

== NMR Data Processing ==

{| class="FCK__ShowTableBorders" cellspacing="1"
|- valign="top"
|
NMRPipe

*[[Brief description of philosophy, commands, and functions of NMRPipe|Brief description of philosophy, commands, and functions]]
*[[Routine 2D Experiment|2D experiments]]
*[[Routine Processing Procedure for 3D 15N and 13C-edited Experiments|3D 15N and 13C-edited experiments]]
*[https://rustednail56.wixsite.com/jomadjeans HSQCTROSY] RDC Measurement|2D ]][[HSQCTROSY RDC Measurement|15]][[HSQCTROSY RDC Measurement|N HSQC-TROSY experiment for RDC measurement
*[https://rustednail56.wixsite.com/jomadjeansforwomen Jmodulation] Experiment RDC|2D J-modulation experiment for RDC measurement
*[https://www.kiwibox.com/JOMAD_Jeans/ Alignment] Media Preparation|Alignment Media Preparation for RDC measurement

|
Other

*[[Processing NMR spectra with PROSA|PROSA]]
*[[Bruker Data Processing|TOPSPIN]]
*[https://www.jomadjeans.com/collection/all Fall Jeans]
*[[Processing non-uniformly sampled spectra with Multidimensional Decomposition|Processing NUS spectra with MDD]]
*[https://www.jomadjeans.com/collection/all Spring Jeans]

|}

== NMR Resonance Assignment ==

*[[Resonance Assignment/Principles and concepts|Principles and concepts]]

{| class="FCK__ShowTableBorders" cellspacing="1"
|- valign="top"
|
*Semi-automated protocols
**[[Resonance Assignment/CARA|CARA]]
**[[Sparky]]
**[[Resonance Assignment/XEASY|XEASY]]

|
*Automated resonance assignment
**[[AutoAssign|AutoAssign]]
**[[AutoAssign WebServer|AutoAssign server]]
**[[Abacus|ABACUS]]
**[[The PINE Server|PINE server]]

|
*Validation and deposition
**[[AVS|Assignment validation suite (AVS)]]
**[[LACS|Linear analysis of chemical shift (LACS)]]
**[[PDB and BMRB Deposition#Preparing_files_for_BMRB_depostion|Depositing chemical shifts]]

|}

== Structure Calculation and Validation ==

[[Structure Calculation and Validation|Principles and concepts]]

{| class="FCK__ShowTableBorders" cellspacing="1"
|- valign="top"
|
*Structure calculation
**[[CYANA Structure Determination Program|CYANA]]
**[[AutoStructure Structure Determination Program|AutoStructure]]
**[[Structure Calculation Using CS-Rosetta|CS-ROSETTA]]
**[[Structure Calculation Using CS-DP ROSETTA|CS-DP ROSETTA]]
**[[Structure Calculation Using CS-RDC-ROSETTA|CS-RDC-ROSETTA]]
**[[Consensus Approaches|"Consensus" approaches]]
**[[Refinement Strategies|Refinement Strategies]]

|
*Special topics
**[[Protein-Ligand Complexes|Protein-Ligand complexes]]
**[[Working With Metal Ions|Metal ions]]
**[[Residual Dipolar Couplings in Structure Refinement|Residual Dipolar Couplings]]
**[[REDCAT|REDCAT]] and [[REDCRAFT|REDCRAFT]]
**[[Paramagnetic Constraints in Structure Determination|Paramagnetic constraints]]
**[[RDC-Assisted Dimer Structure Determination|RDC-assisted dimer structure calculation]]

|
*Structure Refinement
**[[Structure Refinement Using CNS Energy Minimization With Explicit Water|CNS refinement]]
**[[Structure Refinement Using XPLOR-NIH|XPLOR-NIH refinement]]
**[[Rosetta High Resolution Protein Structure Refinement Protocol|ROSETTA refinement]] 

|
*Validation and deposition
**[[PdbStat|PdbStat]]
**[[PSVS|PSVS]]
**[[RPF Analysis|RPF analysis]]
**[[MolProbity Server|MolProbity server]]
**[[RDCvis & KiNG|RDCvis]]
**[[PDB and BMRB Deposition|PDB and BMRB deposition]]
**[[ADIT-NMR|ADIT-NMR]]
**[[HarvestDB|HarvestDB]]
**[[SPINS|SPINS]]

|}

== nmr 2.0 ==

[[http://www.nmr2.buffalo.edu/ Homepage]]

{| class="FCK__ShowTableBorders" cellspacing="1"
|- valign="top"
|

*[http://www.nmr2.buffalo.edu/comm/links/ nmr 2.0 Communication]
*[http://www.nmr2.buffalo.edu/resources/edu/ nmr 2.0 Educational]

*[http://www.nmr2.buffalo.edu/resources/jobs/ nmr 2.0 Jobs]
*[http://www.nmr2.buffalo.edu/resources/jobprofiles/ nmr 2.0 Job Seekers]

*[http://www.nmr2.buffalo.edu/resources/poll/ nmr 2.0 News]

*[http://www.nmr2.buffalo.edu/resources/queries/ nmr 2.0 Queries]

*[http://www.nmr2.buffalo.edu/resources/humor/ nmr 2.0 Humor]

*[http://www.nmr2.buffalo.edu/resources/links/ nmr 2.0 Links]

*[http://www.nmr2.buffalo.edu/blog nmr 2.0 Blog]

|}

For a more linear view of the contents including those in development see [[Wiki Tree Layout]]

Main Page

2017-11-06T19:24:19Z

Pwils3:

__NOTOC__

<big>'''Welcome to the NESG Wiki!'''</big> 

The NESG Wiki is a medium for sharing experimental protocols as well as training an educational materials in the fields of structural biology, structural genomics and biomolecular NMR.

Please check out [[NESG NMR wiki workshop at the 2010 Keystone meeting|NESG NMR wiki workshop presentations at the 2010 Keystone meeting]]

== Protein Sample Production ==

{| cellspacing="1" class="FCK__ShowTableBorders"
|- valign="top"
|
*[[Target selection|NESG target selection]] 
*[[DNA cloning protocols|DNA cloning protocols]] 
*[[Protein purification|Protein expression and purification protocols]]  
*Sample Optimization
**[[Construct optimization]]
**[[Buffer optimization]]
**[[Cofactor optimization]]

|
*Protein Sample Analysis
**[[SDS page gel]]
**[[Protein concentration|Protein concentration measurements]]
**[[Oligomerization Status|Assessment of Oligomerization State]]
***[[Gel filtration and light scattering|gel-filtration and light scattering]]
***[[NMR determined Rotational correlation time]]
**[[MassSpectrometry|Mass spectrum]]
**[[NMR screening]]

 

|}

== NMR Data Acquisition ==

{| class="FCK__ShowTableBorders" cellspacing="1"
|- valign="top"
|
*Routine operation
**[[NMR Sample Preparation]]
**[[Inserting NMR Sample]]
**[[Tuning and matching]]
**[[Deuterium Lock]]
**[[Shimming]]
**[[Pulse width calibration]]
**[[Temperature calibration]]
**[[Chemical shift referencing]]
*Advanced operation
**[[Deuterium pulse width calibration and decoupling]]

|
*NMR data acquisition for protein structure determination
**[[Common NMR experiment sets]]
**[[NMR experiment setup scripts for VNMRJ|Custom NMR experiment setup scripts for VNMRJ]]
**[[Estimation of rotational correlation time]]
**[https://www.jomadjeans.com High waisted flare jeans]
**[[Simultaneous 13C,15N-resolved NOESY]]
**[[2D (13C, 1H) HSQC for fractionally 13C-labeled samples|2D [13C, 1H]-HSQC for fractionally 13C-labeled samples]]
**[https://www.jomadjeans.com Ankle grazer jeans]
*[[Setting up non-uniformly sampled spectra|Non-uniform sampling (NUS) ]]
**[https://www.jomadjeans.com designer jeans for women]
**[[Setting up non-uniformly sampled spectra/NUS guide for Bruker according to Arrowsmith group in Toronto|NUS - Bruker]]

|
*Maintenance (VARIAN)
**[[Installing and updating BioPack]]
**[http://prime.ece.mtu.edu/wiki/index.php?title=User:Jomadjeans Full probefile calibration]
**[[Rebooting spectrometer console]]
**[http://jomadjeansdesignerjeansforwomen.wikidot.com Conditioning procedure for cryogenic probes]

|}

== NMR Data Processing ==

{| class="FCK__ShowTableBorders" cellspacing="1"
|- valign="top"
|
NMRPipe

*[[Brief description of philosophy, commands, and functions of NMRPipe|Brief description of philosophy, commands, and functions]]
*[[Routine 2D Experiment|2D experiments]]
*[[Routine Processing Procedure for 3D 15N and 13C-edited Experiments|3D 15N and 13C-edited experiments]]
*[https://rustednail56.wixsite.com/jomadjeans HSQCTROSY] RDC Measurement|2D ]][[HSQCTROSY RDC Measurement|15]][[HSQCTROSY RDC Measurement|N HSQC-TROSY experiment for RDC measurement
*[[Jmodulation Experiment RDC|2D J-modulation experiment for RDC measurement]]
*[https://www.kiwibox.com/JOMAD_Jeans/ Alignment] Media Preparation|Alignment Media Preparation for RDC measurement

|
Other

*[[Processing NMR spectra with PROSA|PROSA]]
*[[Bruker Data Processing|TOPSPIN]]
*[https://www.jomadjeans.com/collection/all Fall Jeans]
*[[Processing non-uniformly sampled spectra with Multidimensional Decomposition|Processing NUS spectra with MDD]]
*[https://www.jomadjeans.com/collection/all Spring Jeans]

|}

== NMR Resonance Assignment ==

*[[Resonance Assignment/Principles and concepts|Principles and concepts]]

{| class="FCK__ShowTableBorders" cellspacing="1"
|- valign="top"
|
*Semi-automated protocols
**[[Resonance Assignment/CARA|CARA]]
**[[Sparky]]
**[[Resonance Assignment/XEASY|XEASY]]

|
*Automated resonance assignment
**[[AutoAssign|AutoAssign]]
**[[AutoAssign WebServer|AutoAssign server]]
**[[Abacus|ABACUS]]
**[[The PINE Server|PINE server]]

|
*Validation and deposition
**[[AVS|Assignment validation suite (AVS)]]
**[[LACS|Linear analysis of chemical shift (LACS)]]
**[[PDB and BMRB Deposition#Preparing_files_for_BMRB_depostion|Depositing chemical shifts]]

|}

== Structure Calculation and Validation ==

[[Structure Calculation and Validation|Principles and concepts]]

{| class="FCK__ShowTableBorders" cellspacing="1"
|- valign="top"
|
*Structure calculation
**[[CYANA Structure Determination Program|CYANA]]
**[[AutoStructure Structure Determination Program|AutoStructure]]
**[[Structure Calculation Using CS-Rosetta|CS-ROSETTA]]
**[[Structure Calculation Using CS-DP ROSETTA|CS-DP ROSETTA]]
**[[Structure Calculation Using CS-RDC-ROSETTA|CS-RDC-ROSETTA]]
**[[Consensus Approaches|"Consensus" approaches]]
**[[Refinement Strategies|Refinement Strategies]]

|
*Special topics
**[[Protein-Ligand Complexes|Protein-Ligand complexes]]
**[[Working With Metal Ions|Metal ions]]
**[[Residual Dipolar Couplings in Structure Refinement|Residual Dipolar Couplings]]
**[[REDCAT|REDCAT]] and [[REDCRAFT|REDCRAFT]]
**[[Paramagnetic Constraints in Structure Determination|Paramagnetic constraints]]
**[[RDC-Assisted Dimer Structure Determination|RDC-assisted dimer structure calculation]]

|
*Structure Refinement
**[[Structure Refinement Using CNS Energy Minimization With Explicit Water|CNS refinement]]
**[[Structure Refinement Using XPLOR-NIH|XPLOR-NIH refinement]]
**[[Rosetta High Resolution Protein Structure Refinement Protocol|ROSETTA refinement]] 

|
*Validation and deposition
**[[PdbStat|PdbStat]]
**[[PSVS|PSVS]]
**[[RPF Analysis|RPF analysis]]
**[[MolProbity Server|MolProbity server]]
**[[RDCvis & KiNG|RDCvis]]
**[[PDB and BMRB Deposition|PDB and BMRB deposition]]
**[[ADIT-NMR|ADIT-NMR]]
**[[HarvestDB|HarvestDB]]
**[[SPINS|SPINS]]

|}

== nmr 2.0 ==

[[http://www.nmr2.buffalo.edu/ Homepage]]

{| class="FCK__ShowTableBorders" cellspacing="1"
|- valign="top"
|

*[http://www.nmr2.buffalo.edu/comm/links/ nmr 2.0 Communication]
*[http://www.nmr2.buffalo.edu/resources/edu/ nmr 2.0 Educational]

*[http://www.nmr2.buffalo.edu/resources/jobs/ nmr 2.0 Jobs]
*[http://www.nmr2.buffalo.edu/resources/jobprofiles/ nmr 2.0 Job Seekers]

*[http://www.nmr2.buffalo.edu/resources/poll/ nmr 2.0 News]

*[http://www.nmr2.buffalo.edu/resources/queries/ nmr 2.0 Queries]

*[http://www.nmr2.buffalo.edu/resources/humor/ nmr 2.0 Humor]

*[http://www.nmr2.buffalo.edu/resources/links/ nmr 2.0 Links]

*[http://www.nmr2.buffalo.edu/blog nmr 2.0 Blog]

|}

For a more linear view of the contents including those in development see [[Wiki Tree Layout]]

User talk:Pwils3

2017-10-30T16:33:03Z

Pwils3: Created page with 'Pwils3 NESG Talk Page My Website My Blog [https://www.jomadjeans.com Buy Jeans]'

Pwils3 NESG Talk Page

My Website
My Blog
[https://www.jomadjeans.com Buy Jeans]

User:Pwils3

2017-10-30T16:24:24Z

Pwils3: Created page with 'JOMAD Jeans If you are looking for the best [https://www.jomadjeans.com designer jeans for women], look no further than [http://jomadjeansdesignerjeansforwomen.wikidot.com JOMAD …'

JOMAD Jeans If you are looking for the best [https://www.jomadjeans.com designer jeans for women], look no further than [http://jomadjeansdesignerjeansforwomen.wikidot.com JOMAD Jeans]; located in NYC. We offer fits and styles matching whatever season you find yourself in. VAGABOUND - a high waist or midrise jean with optional distressed or ripped elements. You can get skinny ankle or even a zipped ankle on these Jeans. We also have our DRIFTER model. These are athletic fit jeans- and simply the best fitting for women. These designer premium stretch denim provide unrivaled comfort and slim fit on these jeans. The color variety is amazing as well; Interested in destroyed skinny jeans? Check. High waisted flare jeans? Check. Designer ankle grazer jeans? Of course. We have all the designer inventory if you ever choose to buy jeans. If you are vertically challenged, we have jeans for short women. If you are taller, look no further than our long, high waisted fits. Our rebound denim is among the most comfortable and provides women with the best fitting jeans. They have a [https://www.jomadjeans.com skinny fit jeans], and the denim fits slim and snug. We are located in New York City, but don't Hesitate to visit our store online.

We wander because we wonder. We are constantly on the move, feeding a curiosity about the world that can’t be tamed. We are classy, yet cool. Modest, yet modern. Our style is as dynamic as our lifestyle.
Inspired by the nomadic lifestyle of our ancestors, JOMAD Jeans was created as a brand for people who want to live freely. Nothing–especially not clothing– should hold us back from the journey that lies ahead.

The '''Gypsy''' is a mid-rise skinny ankle jean crafted from ultimate rebound denim. Slimming fit while giving you the vintage attitude. Five-pocket styling with a zip fly and button closure

The '''Drifter''' is a high-rise kickboot jean that fits like a skinny jean through the hip and knee and then breaks into a subtle kickboot at the hem. Crafted from a ultimate stretch denim with holding power