The Coot User Manual.iStat Menus version history

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
UNK the,. of and in ” a to was is) (for as on by he with ‘s that at from his it an were are which this also be has or: had first one their its new after but who not they have. What is Coot? Coot is a molecular graphics application. Its primary focus is crystallographic macromolecular model-building and manipulation rather than representation i.e. more like Frodo than Rasmol. Having said that, Coot can work with small molecule (SHELXL) and electron microscopy data, be used for homology modelling, make passably pretty pictures and display . UNK the,. of and in ” a to was is) (for as on by he with ‘s that at from his it an were are which this also be has or: had first one their its new after but who not they have.
 
 

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Next: Introduction , Up: dir [ Contents ][ Index ]. This document is the Coot User Manual, giving an overview of the interactive features. These documents should be distributed with the source code. Next: What is Coot? Coot is a molecular graphics application. Its primary focus is crystallographic macromolecular model-building and manipulation rather than representation i.

Coot is Free Software. You can give it away. The code is designed to be portable to any Unix-like operating system. There is also a Window port called WinCoot. If you want to port to some other operating system, you are welcome 4. Coot works best with a 3-button mouse and works better if it has a scroll-wheel too see Chapter 2 for more details 5. Rather that using the GUI to read in information, you can use the following command line arguments:.

There you can read more about the CCP4 molecular graphics project in general and other projects which are important for Coot 7. Whenever Coot manipulates the model, it saves a backup pdb file. There are backup files in the directory coot-backup 8. I would like to know about coot crashing 9 so that I can fix it as soon as possible.

If you want your problem fixed, this involves some work on your part sadly. First please make sure that you are using the most recent version of coot. I will often need to know as much as possible about what you did to cause the bug. If you can reproduce the bug and send me the files that are needed to cause it, I can almost certainly fix it 10 – especially if you use the debugger gdb and send a backtrace too When there is no map, using the scroll-wheel has no effect.

If there is exactly one map displayed, the scroll-wheel will change the contour level of that map. Select atoms with the Left-mouse. Use the scripting function quanta-buttons to make the mouse functions more like other molecular graphics programs to which you may be more accustomed You may not completely like the way the molecule is moved by the mouse movement To do this from the scripting interface: vt-surface 1 If you do want screen-z rotation screen-z rotation, you can either use Shift Right-Mouse Drag or set the Virtual Trackball to Spherical Surface mode and move the mouse along the bottom edge of the screen.

Many functions have tooltips 16 describing the particular features and are documented in Chapter Modelling and Building. On restarting Coot, it should be in antialias mode Coot is based on the concept of molecules.

Maps and coordinates are different representations of molecules. The access to the molecule is via the molecule number. It is often important therefore to know the molecule number of a particular molecule. The Molecule Number of a molecule can be found by clicking on an atom of that molecule if it has coordinates of course.

The first number in brackets in the resulting text in the status bar and console is the Molecule Number. It is considerably smoother i. The view is orthographic i.

It is easily changed see Section Clipping Manipulation. The angle between the stereo pairs the stereo separation can be changed to suit your personal tastes using:. When asked to pick a residue or atom, the cursor changes from the normal arrow shape to a “pick” cursor. Sometimes it is difficult to see the default pick cursor, so you can change it using the function.

The cursors can be viewed using an external X program:. It can be removed using:. Note that in side by side stereo mode you only get the left-hand image. Use something like:. Here you can select which maps and molecules you can see and how they are drawn The “Scroll” radio buttons sets which map is has its contour level changed by scrolling the mouse scroll wheel.

By default, the path names of the files are not displayed in the Display Manager. To turn them on:. You might not want to have the right-hand-side vertical toolbar that contains icons for some modelling operations 21 displayed:. If you want to add to the extensions, the following functions are available:. If you want the fileselection to be filtered without having to use the “Filter” button, use the scripting function.

If you like your files initially sorted by date rather than lexicographically, which is the default use:. Some people prefer that the fileselection for saving coordinates starts in the original directory rather than the directory from which they last imported coordinates.

This option is for them:. There is an compile-time option of adding a script interpreter. Currently the options are python and guile. It seems possible that in future you will be able to use both in the same executable. The binary distribution of Coot are linked with guile, others with python. Hundreds of commands are made available for use in scripting by using SWIG, some of which are documented here. Other functions documented less well, but descriptions for them can be found at the end of this manual.

Note that you type the commands in the upper entry widget and the command gets echoed in red and the return value and any output is displayed in the text widget lower green. The typed command should be terminated with a carriage return To execute a script file from the command line use the –script filename arguments except when also using the command line argument –no-graphics , in which case you should use -s filename.

After you have used the scripting window, you may have noticed that you can no longer kill Coot by using Ctrl-C in the console. To recover this ability:. Coot has an optional embedded python interpreter. Thus the full power of python is available to you. This file should contain python commands that set your personal preferences. The scripting functions described in this manual are formatted suitable for use with guile, i. The scheme interpreter is made available by embedding guile.

This file should contain scheme commands that set your personal preferences. This state file contains information about the screen centre, the clipping, colour map rotation size, the symmetry radius, and other molecule related parameters such as filename, column labels, coordinate filename etc. A state file can be saved at any time using save-state which saves to file 0-coot. Use set-run-state-file-status i to change the behaviour: i is 0 to never run this state file at startup, i is 1 to get a dialog option this is the default and i is 2 to run the commands without question.

How do they do that? By default, each time a modification is made to a model, the old coordinates are written out The backups are kept in a backup directory and are tagged with the date and the history number lower numbers are more ancient Further Undo operations will continue to apply to this molecule until there are none left.

If for reasons of strange system 29 requirements you want to remove the path components of the backup file name you can do so using:. This is not available immediately after a modification This file should contain your most recent edits. In such a case, it is sensible for neatness purposes to immediately save the coordinates probably to the current directory so that you are not modifying a file in the backup directory. It is sometimes useful to use this to orient the view and export this orientation to other programs.

The orientation matrix of the view can be displayed in the console using:. Occasionally you may want to know the space group of a particular molecule.

Interactively for maps you can see it using the Map Properties button in the Molecule Display Control dialog. There is a scripting interface function that returns the space group for a given molecule 32 :. To show the symmetry operators of a particular molecule use: get-symmetry imol which will return a list of strings.

Sometimes molecular replacement solutions for example create models with chains non-optimally placed relative to each other – a symmetry-related copy would be more apealling but would be equivalent, crystalographically. For example, to move the B chain to a symmetry-related position:.

You can also use this dialog to speed it up a bit by decreasing the number of steps instead of turning it off. Coot and linearly interpolate between the views. The clipping planes a. There is only one parameter to change and it affects both the front and the back clipping planes The default is 0. There is a pink pointer at the centre of the screen that marks the rotation centre.

The green axes showing the orientation of the molecule are displayed by default.

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