Click on Zoom In a few times to, well, zoom in. To calculate a data collection strategy to maximize anomalous pairs e. Can I index on peaks collected from several contiguous frames? Now you are ready to integrate the data. Scalepack is the program that does the scaling. Starting the Program and Setting the Data Sets. Go to the Integration Tab to start integration. Someone told me to gradually increase the resolution and alternate cycles of fitting a few parameters.
The blue boxes mark the individual blocks of data. What are all those the Refinement Information values for, and what do they mean?
Scroll down in the graphical data tables to see manul statistics with resolution or by frame number. Experimenters that perform non-commercial research may freely use the program for data evaluation and processing, while collecting data at the beamline. Macromolecular Crystallography, part A, p. Although this manual reflects the most current information possible, you should read the Latest News for information that may not have been available prior to our documentation being finalized.
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.
To remove them use the scripting function;. If you move the Pointer e. The ticks are at 1. Positions in 3D space can be annotated with 3D text. It is often better to use a map that is more realistic and stop the picture whizzing round.
It is best not to have other widgets overlaying the GL canvas as you do this. The contouring elapsed time 37 gives an indication of CPU performance. This will go away in due course.
You are advised to run Coot so that you can see the console and the graphics window at the same time, since feedback from atom clicking for example is often written there rather than displayed in the graphics window. Immediately after the coordinates have been read, the view is by default recentred to the centre of this new molecule and the molecule is displayed.
The recentring of the view after the coordinates have been read can be turned off by unclicking the "Recentre? To disable the recentring of the view on reading a coordinates file via scripting, use: set-recentre-on-read-pdb 0. And that affects just the reading of filename and not subsequent files. By default coot does not allow reading coordinates with duplicated sequence numbers.
To enable the reading of files with duplicated sequence numbers use the function:. The space group should be one of the xHM symbols listed for example in the CCP4 dictionary file syminfo. So, for example, "R 3 2 :H" should be used in preference to "H32".
The reading multiple files using the GUI is not available at the moment. However the following scripting functions are available:. Typical usage of this might be:. Alternatively you can specify the files to be opened on the command line when you start coot see Section Command Line Arguments. SHELX ". ShelxL atoms with negative PART numbers are given alternative configuration identifiers in lower case. Information about about a particular atom is displayed in the text console when you click using middle-mouse.
Do the same to toggle off the label. The newly centred atom is labelled by default. To turn this off use:. The atom colouring system in coot is unsophisticated. Typically, atoms are coloured by element: carbons are yellow, oxygens red, nitrogens blue, hydrogens white and everything else green see Section Display Manager for colour by chain.
However, it is useful to be able to distinguish different molecules by colour, so by default coot rotates the colour map of the atoms i. The amount of the rotation depends on the molecule number and a user-settable parameter:. Also one is able to select only the Carbon atoms to change colour in this manner: set-colour-map-rotation-on-read-pdb-c-only-flag 1.
The represention style of the molecule that has the active residue if any can be changed using the scroll wheel with Ctrl and Shift. The thickness width of bonds of individual molecules can be changed.
This can be done via the Bond Parameters dialog or the scripting interface:. The default thickness is 3 pixels. The bond thickness also applies to the symmetry atoms of the molecule. The default bond thickness for new molecules can be set using:. It is important to understand that these ghosts are for displaying differences of NCS-related molecules by structure superposition, not displaying neighbouring NCS related molecules.
Sometimes SSM does not provide a good or even useful matrix. In that case, we can specify the residue range ourselves and let the LSQ algorithm provide the matrix. Typical usage: manual-ncs-ghosts 0 1 10 list "A" "B" "C". Coot can use the relative transformations of the NCS-related molecules in a coordinates molecule to transform maps.
Note also that the internal representation of the map is not transformed. If you try to export a NCS overlay map you will get an untransformed map. A transformed map only makes sense around a given point and when using transformed maps in Coot, this reference point is changed on the fly, thus allowing map transformations on the fly. You need to turn on symmetry for molecule imol and set the displayed symmetry object type to "Display Near Chains".
Coot provides the possibility to download coordinates from an OCA A pop-up entry box is displayed into which you can type a PDB accession code. Coot will then connect to the web server and transfer the file. The downloaded coordinates are saved into a directory called coot-download. It is also possible to download mmCIF data and generate a map. This currently requires a properly formatted database structure factors mmCIF file Using this function we have the ability to download coordinates and view the map from structures in the Electron Density Server EDS at Uppsala University.
This is a much more robust and faster way to see maps from deposited structures. This function can be found under the File menu item. This feature was added with the assistance of Gerard Kleywegt.
D 60, As well as the molecule number, there is the molecule name - very frequently the name of the file that was read in to generate the coordinates in coot initially.
However, this is only a molecule name and should not be confused with the filename to which the coordinates are saved. The coordinates filename can be selected using the Select Filename… button. If your filename ends in. If for some reason, the pdb file that you read does not have a space group, or has the wrong space group, then you can set it using the following function:.
By default anisotropic atom information is not represented You cannot currently display thermal ellipsoids 47 for isotropic atoms. Symmetry atoms can be labeled Every time you recentre, the symmetry coordinates are updated.
The information shown contains the atom information and the symmetry operation number and translations needed to generate the atom in that position. Coot generates symmetry related atoms by moving the current set close to the origin by a translation, performing the symmetry expansion around the origin and moving the the symmetry coordinates back by applying the inverse of the origin translation.
The origin translation is also displayed in curly braces, e. Sometimes rarely coot misses symmetry-related molecules that should be displayed. In that case you need to expand the shift search the default is 1 :. The protein is represented by one letter codes and coloured according to secondary structure. These one letter codes are active - if you click on them, they will change the centre of the graphics window - in much the same way as clicking on a residue in the Ramachandran plot.
Use can use this to cut and paste into other applications:. Contacts to other residues are shown and to symmetry-related atoms if symmetry is being displayed. The contacts are coloured by atom type The result is displayed graphically, and written to the console. There is no internal mechanism to change the radius according to atom type. With some cleverness you might be able to call this function several times and change the radius according to the atom selection.
There is a function to clear up the dots for a particular molecule imol and dots set identifier dots-handle. There is a function to return how many dots sets there are for a particular molecule imol :. Coot can be used to calculate the mean average and median temperatures factors:.
You can specify the specific chains that you wish to match using the "Use Specific Chain" check-button. Otherwise, move-copy-flag should be 0. Here, imol-ligand is the molecule number of the ligand which is presumed to be a a molecule on its own - Coot simply takes the first residue that it finds.
When activated, the dialog "stays on top" of the main graphics window Some people think that this is not always desirable, so this behaviour can be undone using:. The geometrical restraints are, by default, bonds, angles, planes and non-bonded contacts. Truth to tell, this has not been successful in my hands sadly. Coot then regularizes the residue range. At the end Coot, displays the intermediate atoms in white and also displays a dialog, in which you can accept or reject this regularization.
Use, for example, set-matrix The higher the number the more weight that is given to the map terms The default is This will be needed for maps generated from data not on or close to the absolute scale or maps that have been scaled for example so that the sigma level has been scaled to 1.
Pressing A on the keyboard while selecting an atom in a residue will automatically create a residue range with that residue in the middle.
By default the zone is extended one residue either size of the central residue. This can be changed to 2 either side using set-refine-auto-range-step 2. Intermediate white atoms can be moved around with the mouse click and drag with left-mouse, by default. Refinement will proceed from the new atom positions when the mouse button is released. In more up to date versions, Coot will display colour patches something like a traffic light system representing the chi squared values of each of types of geometric feature refined.
A selection of than 20 residues will not be regularized or refined. The limit can be changed using the scripting function: e. The geometry description for residues, monomers and links used by Coot are in the standard mmCIF format. By default, the geometry dictionary entries for only the standard residues are read in at the start It may be that your particular ligand is not amongst these.
There is a selector in the cif dictionary file chooser that allow you to select the molecule to which molecule refers. Each of the indididual molecules can be specifically selected. Sphere refinement selects residues within a certain distance of the residue at the centre of the screen and includes them for real space refinement. In this way, one can select residues that are not in a linear range. This technique is useful for refining disulfide bonds and glycosidic linkages.
You will need a python-enabled Coot to do this. The following adds a key binding Shift-R that refines resides that are within 3. You can specify the residues that you want to refine without using a linear or sphere selection usine refine-residues. For example:. Refining carbohydrates monomers should be as straightforward as refining a protein residue. When refining a group of carbohydrates, the situation needs a bit more explanation. For each residue pair with tandem residue numbers specified in the refinement range selection, Coot checks if these residue types are are furanose or pyranose in the dictionary, and if the are both one or the other, then it tries to see if there are any of the 11 link types BETA, BETA, ALPHA and so on specified in the dictionary.
It does this by a distance check of the potentially bonding atoms. If the distance is less than 3. Instead of using a sphere to make a residue selection, you can specify the residues directly using refine-residues , for example:. The UNK residue type is a special residue type to Coot. It has been added for use with Buccaneer. By default, atoms with zero occupancy are moved when refining and regularizing.
This can sometimes be inconvenient. To turn of the movement of atoms with zero occupancy when refining and regularizing:. You can change the map that is used for the fitting and refinement tools using the Select Map The atoms selected in the moving fragment have the same alternate conformation code as the first atom you click.
The axis system of the rotations and translations are the screen coordinates. Alternatively 59 , you can click using left-mouse on an atom in the fragment and drag the fragment around. Use Control Left-mouse to move just one atom, rather than the whole fragment. If you click Control Left-mouse whilst not over an atom then you can rotate the fragment using mouse drag.
To change the rotation point to the centre of the intermediate atoms rather than the second clicked atom , use the setting:. The selection is zone-based So to refine just one residue, click on one atom twice. Sometimes no results are displayed after Rigid Body Fit Zone. This is because the final model positions had too many final atom positions in negative density. If you want to over-rule the default fraction of atoms in the zone that have an acceptable fit 0. Rigid body refinement via Nelder-Mead Simplex minimization is available in Coot.
Simplex refinement has a larger radius of convergence and thus is useful in a position where simple rigid body refinement finds the wrong minimum. However the Simplex algorithm is much slower. Simplex refinement for a residue range start-resno to end-resno inclusive in chain chain-id can be accessed as follows:. If you wanted automatically run a function after a model has been manipulated then you can do so using by creating a function that takes 2 arguments, such as:.
It would of course be far more useful if this function was also passed a list of residues - that is something for the future. Baton build is most useful if a skeleton is already calculated and displayed see Section Skeletonization. When three or more atoms have been built in a chain, Coot will use a prior probability distribution for the next position based on the position of the previous three.
Little crosses are drawn representing directions in which is is possible that the chain goes, and a baton is drawn from the current point to one of these new positions. The list of directions is scored according to the above criterion and sorted so that the most likely is at the top of the list and displayed first as the baton direction.
When starting baton building, be sure to be about 3. So, when trying to baton-build a chain starting at residue 1, centre the screen at about the position of residue 2. It seems like a good idea to increase the map sampling to 2 or even 2. Occasionally, every point is not where you want to position the next atom. In that case you can either shorten or lengthen the baton, or position it yourself using the mouse. If you try to trace a high resolution map 1.
Sometimes especially at loops you can see the direction in which the chain should go, but there is no skeleton see Section Skeletonization is displayed and consequently no guide points in that direction. Accept the atom in the same place as last time and now when the new guide points are displayed, there should be an option to build in a new direction.
The following scenario is not uncommon: you find a nice stretch of density and start baton building in it. After a while you come to a point where you stop dismissing the baton build dialog. You want to go back to where you started and build the other way. How do you do that?
The fragment is defined as a contiguous set of residues numbers. So that you should be sure that other partial fragments which have the same chain id and that are not connected to this fragment have residue numbers that are not contiguous with the fragment you are trying to reverse. Briefly, 6-residue fragments of are generated from a list of high-quality 68 structures. This procedure works well for helices and strands, but less well 69 for less common structural features. Recall that the chain-id needs to be quoted, i.
Click and drag across the button 70 to rotate the moving atoms in the graphics window. Docking sidechains means adding sidechains to a model or fragment that has currently only poly-Ala, where the sequence assignment is unknown. The algorithm uses the shape of the density around the C-beta position to estimate the probability of each sidechain type at that position.
First, a sequence should be assigned from a PIR file to a particular chain-id and model number. Choose the model to build on and then Dock Sequence! If all goes well, the model will be updated with mutated residues and undergo rotamer seach for each of the new residues.
If the sequence alignment is not sufficiently clear, then you will get a dialog suggesting that you extend or improve the fragment. The rotamers are generated 71 from the backbone independent sidechain library of the Richardsons group Each rotamer is generated, rigid body refined and scored according to the fit to the map.
Fitting the second conformation of a dual conformation in this way will often fail - the algorithm will pick the best fit to the density - ignoring the position of the other atoms. This search mode moves the some atoms of the mainchain of the neighbouring residues.
The Ramachandran plot is not used in this fitting algorithm. There is a scripting interface:. This interface will not change residues with insertion codes or alternate conformation. The lowest-rotamer-probability is set to 0. To emphasise, then: it matters on which atom you click!
To edit the rotatable bonds of a ligand using this tool, you will need to have read in the mmCIF dictionary beforehand. You need to click on the torsion-general button, then click 4 atoms that describe the torsion - the first atom will be the base non moving part of the atom tree, on clicking the 4th atom a dialog will pop up with a "Reverse" button.
Move this dialog out of the way and then left mouse click and drag in the main window will rotate the "top" part of the residue round the clicked atoms 2 and 3. When you are happy, click "Accept". If you are torsion generaling a residue that has an alt conf, then the atoms of residue that are moved are those that have the same alt conf as the 4th clicked atom or have an blank alt conf. By default, torsions that move hydrogens are not included.
Only 9 torsion angles are available from the keyboard torsion angle selection. Coot uses the same pepflip scheme as is used in O i. Flip the peptide again to return the atoms to their previous position. The allows the addition alternate dual, triple etc. By default, this provides a choice of rotamer Section Rotamers. If there are not the correct main chain atoms a rotamer choice cannot be provided, and Coot falls back to providing intermediate atoms. The default occupancy for new atoms is 0.
This can be changed by using use slider on the rotamer selection window or by using the scripting function:. The remaining occupancy of the atoms after the new occupancy has been added is split amongst the atoms that existed in the residue before the split. It is important therefore that the residues atoms have sane occupancies before adding an alternative conformation. The default Split Type is to split the whole residue.
If you want the default to be to split a residue after and including the CA, then add to your. It is intended to be a collection of crystallographic knowledge as discussed on the CCP4 mailing list , and elsewhere. It is wider in scope than CCP4 as it may contain information about anything relevant to protein crystallographers, whether methods-related "what is the best program for purpose X? The distribution contains individual program documentation for all programs, both in HTML format and as formatted text for use with the man command.
It is intended that users look at the documentation locally, to ensure compatibility with the locally installed programs and to avoid network traffic. However, documentation for the latest release is also available here:. Before you start using the CCP4 suite from the command line, some directories need to be added to the PATH and some other environment variables need to be set.
Its content is distinct from the program documentation, and while it is becoming increasingly out-of-date it still contains useful background material.
Note that a postscript version of the manual is also distributed as part of the CCP4 suite, along with the LaTeX source code. I am looking at preparing some graphical tutorials inspired by some for the DNA project. Here is a simple one: How to create a new ccp4i project If people like the style, I will do more - Martyn. These have since been developed by Maria Turkenburg with extensive help from Eleanor Dodson, Pryank Patel, Norman Stein and others, into a set of tutorials which is distributed with the suite which is the version to use, for reasons described above.
The tutorials are also available here:. More recently, some Molecular Replacement tutorials were developed for a workshop in Beijing, October
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