Re: Cara Isi Game Ps2 Hdd Matrix
Gaspard Xenos
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In the process of matrix assembly, multivalent extracellular matrix (ECM) proteins are induced to self-associate and to interact with other ECM proteins to form fibrillar networks. Matrix assembly is usually initiated by ECM glycoproteins binding to cell surface receptors, such as fibronectin (FN) dimers binding to α51 integrin. Receptor binding stimulates FN self-association mediated by the N-terminal assembly domain and organizes the actin cytoskeleton to promote cell contractility. FN conformational changes expose additional binding sites that participate in fibril formation and in conversion of fibrils into a stabilized, insoluble form. Once assembled, the FN matrix impacts tissue organization by contributing to the assembly of other ECM proteins. Here, we describe the major steps, molecular interactions, and cellular mechanisms involved in assembling FN dimers into fibrillar matrix while highlighting important issues and major questions that require further investigation.
Use the prefix ? before any label, e.g. ?HA instead of HA. This will indicate to CARA that the assignment is not final. Furthermore, the standard checks for consistency will be switched off for this atom, allowing you to assign several chemical shifts with ?HA. A final assignment of HA is only possible to one atom. pascal
In an ideal case, every spin has exactly the same resonance frequency (or chemical shift) in every spectrum. However due to different experimental or sample conditions, the chemical shift for a given spin may vary between spectra. The "real" chemical shift of a spin is defined the first time it is assigned in a spectrum (say spectrum #1). An Alias can be created for this spin in a spectrum where the shift deviates from the "real value" using "Move Spin Alias" instead of Move Spin. Any other such functions are logical extensions of this concept.
You should use aliases only if really necessary (not to microadjust every peak). This is because when you create an alias in a spectrum the position of peaks involving that spin in the spectrum become independent of the position of the related peak in other spectra. This makes it difficult to detect inconsistencies in your assignments.
The state of your aliases can be checked in the Repository Window->Projects->MyProject?->Spins. Any Spin with a node next to its name has aliases. You can inspect their values in this list by clicking on the node. In spectra, normally peaks are represented by a "+" symbol. Peaks constructed from spins with an alias (in any dimension) are represented with an "x". To remove the alias, select the peak and execute "move alias" without moving the cursor.
Aliases are important for import and export from/to XEASY and for structure calculation software. Instead of importing a chemical shift or peak list you can import an Alias Shift List, that is only valid in the context of a particular spectrum. This is done by executing import alias shifts for the spectrum in question opened with MonoScope. To export the aliases for this spectrum, right-click the spectrum in Projects->MyProject->Spectrum and select Export Atom List.. pascal
A Peak is CARA's representation of a crosspeak. It is fully compatible with XEASY's concept of peaks. It can be associated with a Volume. A peak is always bound to a given spectrum. Peaks don't use most of CARA's advanced functionality, but are useful for integration and interaction with external programs like XEASY or ATNOS/CANDID. Unlike in XEASY, in CARA peaks are generated if at all at the end of a project for integration purposes.
A Spin represents the resonance frequency of a single atom. CARA can link Spins together and show expected peaks in a spectrum even if they were not picked manually, based on the spin system and residue type definitions. Such a dynamically generated peak is "inferred" from the database.
A System is a collection of Spins. If you pick a new System, several Spins are put into the new System (picking a System in an 15N-HSQC yields HN and N Spins). A System can be linked to neighboring systems. pascal
A spin link is CARAs way of representing NOEs or through-space connection between spins. Each spin link contains two entries listing the spin numbers of the two linked spins. Once a spin link is created, a NOE crosspeak will appear in any NOESY spectra displayed with HomoScope, PolyScope, StripScope, and SystemScope where it is expected between the linked spins . Spin links are created automatically in a NOESY spectrum when propose peak is used in the above scopes. If you have a peaklist from an XEASY project, you can also generate spin links for all the proton pairs appearing in each line of the peaklist. See the PolyScope Tutorials for details. Fred
Alexey Neumoin has provided a PDF file which lists shortcuts. You can also do the following: In any Scope, type "?" at the command line and hit return. Then click on "Message Log". You will see all shortcuts for the Scope in the lower right window of the explorer.
The easiest way is to right-click on the project in Cara-explorer and select "Export-Atom List". This will write out the chemical shifts as a "proton list" in xeasy format. If you are doing structure calculations, you will need to write out in a format compatible with the residue library of the program in question. In this case the CALUA script "WriteAssignments.lua" is appropriate. You can select between BMRB, DYANA and CYANA2 formats. This script is also acceptable for writing out a BMRB deposit. If you are analysing the chemical shifts, you may want to write them out with each atom type in a separate column (e.g. all "CA" in one column). In this case, try the CALUA script "WriteShiftsInColumns.lua". A similar script is available for writing out shifts for systems as input to the assignment program PACES. "ExportToPaces.lua". If you are making plots of deviations from random coil shifts then the scripts "ChemShiftDeviationsFile.lua" and "ChemShiftDeviationsPlot.lua" are useful. There are additional scripts available for other applications.
The easiest way is to shift-click at the left edge of the peak in the slice window and drag the mouse to the right edge. The width is displayed on the status line. w 0.041 (20.45) means the width is 0.041 ppm or 20.45 Hz.
Serious bugs should be immediately reported via bug tracker. Please include your email address, as much details as possible and attach all pertinent files ( e.g. param files, peaklists, repositories ...).
There is a tradition of programs with womens names in the Wuthrich group (like DIANA). CARA stands for "Computer Aided Resonance Assignment" Don't confuse it with the other CARAs... See the CARAsynonyms.
If you change a .param file using a text editor or XEASY while CARA is running, CARA will not be aware of this change, since it stores the calibration upon loading. You will need to replace the spectrum with itself. Click on the Spectrum in the Spectra-Explorer. Right-click Replace Spectrum and reselect the spectrum to load it again.
A typical situation: You have opened a spectrum with Cara. Then you retransform the spectrum with PROSA and overwrite it. Then you open MonoScope. This may lead to a crash. Since CARA uses a "map" of the spectrum for fast navigation, retransforming and overwriting the spectrum may change this map. The solution is to replace the spectrum with itself. Click on the Spectrum in the Spectra-Explorer. Right-click Replace Spectrum and reselect the spectrum to load it again.
After importing a peaklist, you can rotate it. However as soon as you save it into the repository using Save Peaklist..., CARA considers the orientation to be final. So, the trick is to import, rotate and then save.
Peak inference is a set of algorithms CARA uses to predict the positions of peaks in displayed spectra. It is (currently) active in the following scopes: HomoScope, PolyScope, StripScope, SystemScope. CARA turns the usual paradigm for resonance assignment on its head. Usually (e.g. XEASY) one picks peaks and by comparison of the correlations between different peaks they are eventually assigned a label and finally a residue. CARA from the beginning works with spins which each have a specific ppm value. Peaks are inferred from the spinlist and a knowledge-base which represents the magnetization-transfer pathway for each experiment, the SpectrumTypes?, and an atomic model for each ResidueType. CARA predicts the expected positions of the peaks when the spectrum is displayed. In order for all peaks to be correctly modeled, the label and ResidueType assigned to each spin must be correct. CARA thus continually monitors the consistency of the emerging database of spins and represents this in the form of inferred peaks in the displayed spectra. This scheme also avoids the need to create peaklists for each spectrum and the inevitable problems related to synchronizing these lists. Fred
ave is the statistically-averaged chemical shift for a given atom from a ResidueType (usually the BMRB database value). dev is the range of deviations from ave which are considered close enough so that the shift of a given spin "matches" the statistically expected range for the atom that it is assigned to. The closer the shift is to ave, the higher the fitness of the match. Spins outside of dev, make zero fitness contribution in a fragment alignment. SDmult is the multiplier used by the script "LoadBmrbStats.lua" to calculate dev from the standard deviation of the BMRB database. E.g. the default value for SDmult = 4 meaning that dev = 4 SD where SD is the BMRB standard deviation for the chemical shifts assigned to the corresponding Atom in a given ResidueType. When "show alignment" is executed in StripScope, the selected fragment is mapped onto all possible sequence positions and for each position the fitness of every spin whose label matches an atom at the aligned residue position contributes to the total fitness for the fragment mapped at that position. This total fitness determines the ranking of the aligned fragment positions. Fred*
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