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The histogram of the values of fieldname and their lower bounds within their bins in Gaussian distribution will be plotted. Select a field, 2. Set optional parameters and click OK if w is given, nbin will be ignored. The outputs are: filename.

Interface for extra functionality in Gamess. Generates input and reads output for Z-matrix optimisations and electrostatic potential calculation in Gamess.

Author Michael Charlton. There are three main routines you can call : gamin 'gamess. Contour the MEP on a grid around the molecule using a Gui to control the three contour levels. Works with the version of Gamess WinGamess You will need to change the basis set manually but you can select an option in the Gui to perform a B3-LYP calculation. The input file is generated when you enter a file name and press return. This is needed when you come to analyse the results.

There is an option to select a Z-matrix i. This can lead to faster optimisation - I achieved optimisation of 3-Me pyridine in 7 cycles rather than 42 with cartesian, so quite a useful saving.

It is possible to select a partial Z-matrix optimisation in which some degrees of freedom DoFs are frozen at their input values. This is handy for calculating strain energies, where you can freeze all torsion angles and allow the bonds and angles to relax. A Gui is generated which allows interactive selection of the frozen DoFs. The input file for the MEP calculation can also be generated.

This option generates a grid of points around the molecule which can be manipulated using a Gui to give the size of grid you need to observe features of interest. Note : optimisation will move the molecule slightly from the starting point, so you may want to optimise first and then do a second calculation without opt.

Z-matrix optimisation moves the atoms to the co-ordinate origin, so your grid WILL be in the wrong place. The default version of Gamess limits you to only grid points. You will need to recompile it. Go to the source directory in the unpacked distribution and edit prplib. Then save and follow the compilation instructions. Easier on linux than windows as you will need compilers, which only come free with good operating systems.

Database Utility Functions. This script has functions that perform simple but useful database related tasks such as: - select every nth entry in a MOE database - index a group based on a field identifier - select duplicate entries in a specified field - replace exiting entries in a specified field. Author Kaushik Raha. Also: compare the restraints vs current system. It also compares the existing MOE-restraints vs. RingBreed: Breed operation on bisubstituted rings.

Breed operation on aligned structures of A-B-C formula where B is a ring system. For n input structures, it generates all A n -B n -C n combinations. Mark protomers generated by sdwash operations. Marks protomers generated via sdwash operations. Can be used to separate them from tautomers.

The -protomer switch in sdwash creates the tautomers along with protomers. In case enumerating new tautomers from the input structures is undesirable this program can be used to mark the protomers in the enumerated database, so that they can be separated from the tautomers.

Author David Whitley. ParaSurf generates molecular surface properties based on semi-empirical molecular orbital calculations. ParaFit superposes and compares molecules using the spherical harmonic expansions of the molecular surface and properties calculated by ParaSurf. ParaSurf requires the results of semi-empirical molecular orbital calculations, which can be provided either by VAMP or by a public domain version of MOPAC that is available for free download from www.

The distribution is a zip archive containing the SVL scripts, entries for the moe-menus file and a manual in PDF format that provides full details on how to install and use the scripts. Radial Distribution Function Descriptors.

This is an independent implementation of J. This is an independent implementation D. Bondarev of the reference below: J. You can then use MOE fingerprint tools as usual. Prediction of Cytochrome P Reactive Sites. Implementation of the CypScore method to predict positions in drug-like molecules that are likely sites for metabolism by cytochromes P This is an implementation of the CypScore method devised by Hennemann et al. The script processes single molecules loaded in the main MOE window or groups of molecules stored in a molecular database.

Reactivity scores are added to the molecular database and the results can be viewed graphically in the MOE Database Browser. For six oxidation reactions, Hennemann et al. The original paper described a procedure to establish a common reactivity scale for all the models, providing a CypScore value for each atom in the range from 0 stable to reactive , and implemented this procedure for a proprietary data set.

Unfortunately, Hennemann et al. To overcome this, this script employs a common reactivity scale that is a close approximation to the one used by Hennemann et al. Consequently, the results obtained will approximate closely, but not match exactly, those in the original publication.

The distribution is a zip archive containing the SVL script cypscore. Reference: M. Hennemann, A. Friedl, M. Lobell, J. Keldenich, A. Hillisch, T. Clark and A. CypScore: quantitative prediction of reactivity toward cytochromes P based on semiempirical molecular orbital theory. ChemMedChem, , 4. New Features: -essential descriptor option -support non-linear model with lots of SVL functions such as sqr, sqrt, log Author Junichi Goto. Kappa statistic for nonlinear relations.

A nonparametric statistic that can detect linear and nonlinear functional relationships in bivariate data samples. This can be handy for automatically detecting linear and nonlinear relations in samples of points, whereas the usual correlation coefficient may be nearly zero for nonlinear relations. The yfit values form a relatively smooth curve. All this is described in: G. Crippen, Computational Biology and Chemistry, 33, Torsion Editor. Simply run the function, e.

Once the application is running one needs to select two atoms that constitute a rotatable bond. This is done by selecting the first atom then the second atom by holding down the shift key. Atoms attached to the second selected atom will be the ones that move when the bond is rotated Alt - left drag.

The arrowhead points toward the movable portion - to reverse which half of the molecule will rotate click on the Reverse button - to see the current value of the selected torsion toggle on Show meters. Note the values run from degrees to degrees in a clockwise sense when the rotatable atom is in front - to add a torsion to the list, select a valid set of atoms then click on Create. The atoms that comprise the torsion, the original angle when the torsion was added to the list and the current angle is shown.

Now whenever this value changes, it will be updated in the list and the meters as well if Show Meters is toggled on - to reselect a torsion in the list, simply click on it and the corresponding atoms will be selected in MOE - to set a torsion back to its original value, select it in the list and click Reset.

The original torsion angle is value that existed when the torsion was added to the list. If you decide to minimize the system while the editor is running please make sure that no atoms are selected as the application may create sets of fixed atoms. Configure display from 2 molecule fields in a DB browser. Sets environment values for a database so that the database browser, will show the ligand and receptor pocket atoms. The molecules are read from fields for the ligand and receptor.

A score for the docked pose can also be specified. A number of sets of receptor, ligand and scores can be specified. However, a single field can only belong to one of these sets. If you want the same data to appear in different sets for instance a Corporate ID as the score , you need to copy the field. Fields must always be specified for the ligand and receptor. The score field is optional. Save this script to your hard disk. Sequence Similarity Monitor. Show and colour by sequence similarity and identity in the Sequence Editor.

Output alignment and scores to HTML report. Score the sequences in the main MOE window by similarity. The similarity matrix is used from the default setting for the MOE system blosum62 by default , but you can pick a different one from the list. The identity and similarity between two chains is shown in the panel. If you select the "Color Residues" checkbox then the residues will be colored so that similar residues are green and dissimilar residues are red.

If you have any chains selected, the colouring and sequence similarity and identity scores are restricted to selected chains. If you click the "Report" button, then an HTML file is written out with the sequence alignment and the similarity matrix, comparing all the sequences against all the others. This matrix is not symmetrical - in one half of the matrix the scores are divided by the number of amino acids in one sequence.

In the other half of of the matrix, the scores are divided by the length of the other sequence. If you have any residues selected in the Sequence Editor when you click the "Report" button, then the rest of the residues in the same column will be selected. The similarity matrix in the HTML file will only consider the residues in those columns.

In the sequence alignment, the residues which had been selected will be shown in bold and upper case. Unselected residues will be in the normal font and lower case. The rPos residue numbers for the whole alignment and the rUID numbers for the first sequence are shown at the top of the alignment.

In the rPos residue numbering the residue number is shown for the residues where the rPos is a multiple of The residue number is positioned so that the unit digit from the number is above the residue. Residues where the rPos number ends in 5 are shown with a : character. If there is an rINS insertion character for the residue, then this is shown. Otherwise if the rUID number ends in 5, then this is shown with a : character.

If there is another residue it is shown with a - character. If there is a gap in the sequence for that structure, then a space is shown. The rINS value is shown for residue 20A. There are 3 gaps in the alignment, but there are only 2 spaces shown in the rUID numbering line as the label for residue 30 overwrites one of the spaces.

USAGE 1. Save this file to your hard disk. Run this file. Molecular superposition. Cherkasov, Z. Shi, M. Fallahi, G. Chemistry, 48, , Author Artem Cherkasov. Load this file. In the Database Viewer select the Compute Descriptors menu. Select the descriptors the you want to calculate and click the OK button.

Warning: When unparameterised atoms are found, the electronegativity will be set to and the covalent atomic radius to 0. A warning will be printed to the SVL command line.

Secondary Structure Selector. Provides a GUI to highlight areas of secondary structure within a protein and then allows you to de select the residues associated with the region. You can choose which chain you want to select from with the pull-down. The tool then allows you to visualise specific parts of the secondary structure by adjusting the two sliders.

Residues between the sliders red are selected, residues outside the sliders green are unselected. You can skip forward or backward one residue using the single arrow buttons. Once you have identified the feature you are interested in, you can de select the residues in the sequence editor using the buttons at the bottom.

Pressing "done" will return the 2ary structure rendering to how it was when you started. To use the code, load it into Moe and type SSS []. Automatic generation of candidate structures from a pharmacophore pattern.

Author Vincenzo Tschinke. The input for the program is a set of fragments in the three-dimensional orientation corresponding to a given pharmacophore model. The treatment consists in connecting the fragments with spacers assembled from small chemical entities atoms, chains or ring moieties. The results are new structures containing the fragments in the orientation defined in the input. The program offers the opportunity of rapidly applying a pharmacophore model in drug-design by generating automatically a set of chemical sructures conforming to the model.

Tschinke, V. Author Andreas Lambropoulos, Ghislain Deslongchamps. Calculations can be performed on single molecules or on multiple structures in either. Bypassing the cryptic Gaussian command line, various calculations can be performed in GI-MOE including: ground state and transition state calculations 3 methods , checkpoint file restarts, potential scans with or without geometry optimization , full ONIOM implementation 2-layer and 3-layer , frequency calculations, solvation, and automated RESP charge fitting.

Tools for. Calculations can be performed on a local installation of Gaussian or via the GI-MOE remote computing window, which allows for automatic login and submission of GI-MOE jobs to a distributed computing cluster. A complete user manual is provided. Spectral Clustering. Performs spectral clustering, as outlined in M. Brewer, J. Model, 47 , Performs Spectral Clustering, based upon M. Model, 47 , Code written by M. Charlton at Chroma Therapeutics, The code needs the tanimoto metric to be applicable to the FP you select.

The code uses two methods of filtering the clusters, as outlined in the paper. The default "threshold" method using a value of 0. Note on timings : the code uses MOE's eigenvector solution function and can get quite time consuming for large sets, potentially scaling with the third power of the number of compounds. Sample timings 2.

Thaw' a PDB file: performs a steered energy minimization to preserve the active site. A major problems in energy minimization of the raw PDB files is the lack of hydrogen atoms in the crystallographic coordinates.

At this point, a regular energy minimization will lead to significant perturbations and movements of hydrogens as well as the heavy atoms. See the online. Multi-molecule database browser.

Update fixed navigator button sensitivity The inspiration for this application is to create an interactive version of the DBV File Print panel. To use this script, save the file to your hard drive then run it, e. Clicking that button allows one to jump to a specific page number.

The Subject menu allows one to choose a molecule field. Define template allows a common substructure to be entered based on atoms in the main MOE window. To use this, click Define Template, then either build the scaffold using the Builder or simply click a molecule to toggle it into MOE. Select the scaffold atoms and click Load in the "Define Template" window. Set Data Fields allows the user to choose a set of data fields to be shown as text.

Also a numeric field can be shown as a colour-coded square; use the Activity Indicator drop down menu to select the field. The Action button allows the user to change what happens when a molecule is clicked in the Big Browser panel. If Toggle Sel is chosen, the entry selection state will be toggled. If Mark is chosen, the value in the text field will be written to the field specified in the drop down menu' The Clear button clears whatever the action is currently set to, i.

There is no effect for Mark mode. The Grid drop down menu sets the number of molecules depicted; the grid is defined horizontal x vertical. The Size menu sets the size of each cell; 1 is smallest, 5 is largest. Browse Selected sets the browser to show only the entries that were selected when the box was checked. This means that if you are browsing a set of selected molecules and you deselect one of the entries, it will not be removed from the browser.

To remove it, you will need to turn off "Browse Selected" then re-enable the option. The application is not sensitive to changes in the database e. I aim to address this in a future revision. Please send any bug reports or feature requests to sgrimshaw chemcomp. Write conformations for molecules.

Given a database with a molecule identifier, extracts conformations from one or more other databases and writes the output to a new database. There is an option to only write the molecules from the selected entries in the initial database.

A threshold can be set for the size of the output files. New output databases will be created once this limit has been passed. When the script starts, there is a prompt to select the MDB database with the 2D molecules. This needs to have fields with the identifier for the molecule, and the filename which has the conformations.

Next the databases with the conformations should be specified. The data fields in the input files are listed. If some of the fields are selected, only that data will be written to the output. If none of the fields are selected, all will be written to the output, so long as data is present for some of the molecules. Onion-Like Fragmentation. Fragments molecules by cutting out the scaffold and a adjustable number of adjacent bonds.

Author Daniel Butler. The user can develop an SQL statement using their favourite Oracle cartridge and these scripts will generate a 3D SDF from the submitted SQL statement which is a very handy and efficient way to use the MOE tokens available within a given organisation.

If running on linux you may need to run dos2unix on the files for them to work. Daniel Butler. Jan Export to POVray from This code is now obsolete. The POV-Ray program is free and can be obtained from www. POV-Ray is a freeware ray tracing program. It creates spheres for atoms, cylinders for bonds and triangles for surfaces for MOE graphical objects.

The advantage of using a ray tracing program like POV-Ray is that you get much more control over the appearance of the image, with the option to use settings which would be too slow for use in an interactive program.

You can also output the images in any size you like eg for publications, posters or an exhibition stand , with no loss of crispness. At the moment it does not draw anything for a backbone representation. The trace representation is easy cylinders between the CA atoms. The script now handles graphic objects with a dotted, line and solid surfaces. The position of the camera is not exactly correct, so the perspective view looks a little different to the MOE window.

Any suggestions would be gratefully received. The positions of the lights in the POV-Ray scene are also static. Edit the coordinates and add extra lights as you see fit.

You can also modify the textures of the objects with POV-Ray commands eg to make a surface shiny, smooth, bumpy, etc. Load a view in MOE which has the surfaces, atoms and bonds displayed as you want in the output. It will then be loaded the next time that MOE starts. Load the out. Use It is a MOE video recorder, rather than a 'macro recorder'. You can then create a video file from these movie frames. Once you have finished recording, use a third-party program to join the.

Pairwise rmsd. Computes root mean square deviation between conformers of structures in two molecular fields in an MOE database and writes out the optimal superposition. Calculates pairwise rmsd in a database between mols in first two adjacent mol fields or to fields indicated by the fields parameter.

Diversity Analysis between supplier databases. Process many files in batch mode anf calculate the diversity between two databases using clustering and PCA. Author Suzanne Sirois. FlexX-evaluation Wizard. Updated for FlexX 3. Author Marcus Gastreich. The interaction energies per residue are divided into van der Waals and electrostatic contributions as described in Arakawa et al. The Born solvation contributions are also calculated with the constant or distance-independent dielectric constant with the value of 1 if the Generalized Born implicit solvation model is selected as the solvation model.

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Kode Droid on 15 September Kode Droid on 28 Oktober Willy on 28 Oktober Apakah nox player bisa di gunakan di Tv Televisi? Mat on 30 Januari This handful of keyboard shortcuts allows the user to perform all the basic editing operations, and the keys involved all cluster together at the left end of the bottom row of the standard QWERTY keyboard. Early versions of Windows used the IBM standard.

Microsoft later also adopted the Apple key combinations with the introduction of Windows , using the control key as modifier key. Similar patterns of key combinations, later borrowed by others, remain widely available [update] in most GUI text editors, word processors, and file-system browsers.

Then, by holding shift and selecting the copy source elsewhere on the same screen, the copy would be made as soon as the shift was released. Similarly, holding shift and control would copy and cut delete the source. It was dropped, one presumes, because the original Apple and IBM GUIs were not high enough density to permit multiple windows, as were the PARC machines, and so multiple simultaneous windows were rarely used.

Computer-based editing can involve very frequent use of cut-and-paste operations. Most software-suppliers provide several methods for performing such tasks, and this can involve for example key combinations, pulldown menus, pop-up menus, or toolbar buttons.

Whereas cut-and-paste often takes place with a mouse-equivalent in Windows-like GUI environments, it may also occur entirely from the keyboard, especially in UNIX text editors , such as Pico or vi. When a software environment provides cut and paste functionality, a nondestructive operation called copy usually accompanies them; copy places a copy of the selected text in the clipboard without removing it from its original location.

The clipboard usually stays invisible, because the operations of cutting and pasting, while actually independent, usually take place in quick succession, and the user usually needs no assistance in understanding the operation or maintaining mental context.

Some application programs provide a means of viewing, or sometimes even editing, the data on the clipboard. The term "copy-and-paste" refers to the popular, simple method of reproducing text or other data from a source to a destination. It differs from cut and paste in that the original source text or data does not get deleted or removed. The popularity of this method stems from its simplicity and the ease with which users can move data between various applications visually — without resorting to permanent storage.

Once one has copied data into the clipboard , one may paste the contents of the clipboard into a destination document. The X Window System maintains an additional clipboard containing the most recently selected text; middle-clicking pastes the content of this "selection" clipboard into whatever the pointer is on at that time. Most terminal emulators and some other applications support the key combinations Ctrl-Insert to copy and Shift-Insert to paste. The NeXTStep operating system extended the concept of having a single copy buffer by adding a second system-wide find buffer used for searching.

The find buffer is also available in macOS. The functionality comes in handy when for example editing source code. While this might sound a bit complicated at first, it is often much faster than using the find panel, especial when only a few occurrences shall be replaced or when only some of the occurrences shall be replaced. You can apply the symbol to your slides from the style lists. To change the format of just one or some of the bullet or number styles in a list, such as the color or size, place the cursor at the start of the line that you want to change before opening the Bullets and Numbering box.

Your changes will apply only to the selected lines. To adjust the alignment of items in a list, see How do I increase or decrease the space between a bullet or number and the text in a line?

The best way to apply custom list styles to all slides in your presentation is to modify the slide master. Any list customization you make to the slide master will be saved and applied to all your slides.

You can also edit or create one or more slide layouts that include your customized list styles, and add these layouts to your presentation wherever you want to use your list styles. There are a few things you can't do with lists in PowerPoint that you can in other Office programs, such as Word. For example, PowerPoint does not support:.

Defining new number formats you must choose from the default set of styles offered on the Numbered tab in the Bullets and Numbering box. Applying bold, italic, or underline formatting to bullets or numbers any formatting will be applied to the entire selected line or list.

Nested lists you can press Tab or click Increase List Level to create the same effect, but a new indented bullet or number style is not set automatically by PowerPoint. Select a heading below to open it and see the detailed instructions. Check to make sure you're putting bullets or numbers in a Text box, and not a Title box. In a Text box, you get a number or bullet every time you press Enter. In a Title box, the text is expected to be a single line heading or title.

You can use numbers or bullets, but it treats all lines of text as a single line, resulting in a single bullet or number. To stop creating bullets or numbers and return to text, click Bullets or Numbering again to turn it off.

You can also press Enter and then press Backspace to erase the bullet or number. You can then start adding text, or press Enter to add extra empty lines. To create an indented subordinate list within a list, place the cursor at the start of the line that you want to indent, and then on the Home tab, in the Paragraph group, click Increase List Level.

To move text back to a less indented level in the list, place the cursor at the start of the line, and then on the Home tab, in the Paragraph group, click Decrease List Level. To increase or decrease the space between a bullet or number and the text in a line, place the cursor at the start of the line of text.

To view the ruler, on the View tab, in the Show group, click the Ruler check box. On the ruler, click the hanging indent as shown in diagram below and drag to change the space between the bullet or number and the corresponding text.

There are three different markers that appear on the ruler to indicate the indentation defined for a text box. If the paragraph is not bulleted then this indicates the position of the first line of text.

If the paragraph is not bulleted then this indicates the position of the second line and subsequent lines of text.