Coot online manual

A: Nightmare. If you have a recent [ or later for the scheme version, for the python version] Coot, you can do this:. Subsequent rebuilding in coot is difficult though since hydrogens often does not "follow" when you do side chain rebuilding.

For the moment I have quit transfering hydrogens to coot and add the hydrogens every refinement cycle, though it would be good I think if I could see them in coot without bothering about wrong positions.

So these are my specific questions:. A: This fails because for chi angles Coot uses the Refmac dictionary to know what is connected to what if it can.

The work-around is to rename the refmac dictionary so Coot can't find it - which will force Coot to find bond by distance criteria. A: Yes this fails. This would also fix the chi angles problem too of course. A: Well, it's hard to know what's the problem without details - the console should say something.

But when handling the output of shelxl, I suggest you read the. This only needs to be done once as shelxl does not modify these names. It reads in all relevant shelxl files and provides a menu highlighting the problematic areas in the model.

A: After talking about antialiasing with Stuart McNicholas, I discovered a program called nvidia-settings. I found that if I do:. Of course the FPS takes a hit. Q: I still have a ". There is a warning that I should not add commands to this file.

You need to click on the torsion-general icon, 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 [1].

When you are happy, click "Accept". Window focus may be an issue - depending on your setting, the window manager may eat one of your clicks as you change focus between the dialog and the main graphics window this I find annoying and there are instructions in the FAQ on how to turn that off for various systems.

If it doesn't not work, the "Reverse" button should invert the moving and "base" part of the residue. Is there any formula to calculate the number of electrons based on sigma level and peak height, as given in difference map peaks in coot? A: First, go to the Coot wiki and pick up the scheme key bindings. If you want density information at a given cursor point: point at the blob, press the 'g' key which recentres on the biggest density under the cursor.

Q: I have a pair of disulfide bonds which link two monomers in separate asymmetric units. There is a single monomer in the asymmetric unit, and two monomers come together to form disulfides between Cys Cys45, and CysCys When I real-space-refine these residues, they do not form a nice disulfide, and Coot does not seem to recognize them as a disulfide. Do they need to be written in Python or another language that I had not heard of before? Where can I find a low level description of how to write macros with some examples I know nothing about Python, except that it is fashionable?

A: The other language is a form of Lisp, called Scheme. You can learn about programming python in many ways of course not least the python tutorial , which is what I read first. The coot python extensions are described in the documentation. There is a standard trivial formatting change that has to be made to get the syntax right for python, see "Python Scripting" [ [1] ]. There is a growing collection of coot scripts in this Wiki article. Q: Do an LSQ superposition using specified residues in multiple chains superposing one oligomer on another.

A: That is more involved - and more useful because it can be dynamic. Something like the following perhaps in Scheme, just for amusement not tested. You will need to set imol-ref, perhaps by reading in the reference pdb, as demonstrated below. The function is bound to Shift-Y. Q: We've noticed a new behavior in real space refinement in coot 0. This seems to be described in the release notes by:. Q: I'm wondering why this was changed. Does the optimum elasticity change with resolution, map quality, or another experimental limitation?

Or does it more of a user preference? A residue range can be assigned a sequence and optionally fitted to the map. This is useful converting a poly-ALA model to the correct sequence Multiple mutations are also supported via the scripting interface. Unlike the single residue mutation function, a residue type match will prevent a modification of the residue Two functions are provided: To mutate a whole chain, use mutate-chain imol chain-id sequence where:.

Note that the number of residues in the sequence chain and those in the chain of the protein must match exactly i. Again, the length of the sequence must correspond to the residue range length. Note also that this is a protein sequence - not nucleic acid.

Sometimes one might like to model post-translational or other such modifications. How is that done, if the new residue type is not one of the standard residue types? This imports a model residue for the new residue type and overlays it on to the given residue by using graph-matching to determine the equivalent atoms. Note that if you are replacing are conventional protein residue with a modified form e. The function combines Mutation and Auto Fit Rotamer and is the easiest way to make a mutation and then fit to the map.

There is also a scripting interface:. The resulting molecule will be moved so that it placed at the current screen centre. This procedure creates a pdb file monomer-XXX. A future invocation of Get Monomer uses these file so that the monomer appears quickly You are offered a selection of maps to search you can only choose one at a time and a selection of molecules that act as a mask to this map.

Finally you must choose which ligand types you are going to search for in this map Only molecules with less than atoms are suggested as potential ligands. If you do not have any molecules with less that atoms loaded in Coot, you will get the message:. New ligands are placed where the map density is and protein mask atoms are not.

The masked map is searched for clusters using a default cut-off of 1. In weak density this cut-off may be too high and in such a case the cut-off value can be changed using something such as:.

However, if the map to be searched for ligands is a difference map, a cluster level of 2. Each ligand is fitted with rigid body refinement to each potential ligand site in the map and the best one for each site selected and written out as a pdb file.

The clusters are sorted by size, the biggest one first with an index of 0. Each of these conformations will be fitted to each of the potential ligand sites in the map and the best one will be selected again, if it passes the fitting criteria above. Generally speaking, The more the number of rotatable bonds, the bigger this number should be.

By default the options to change these values are not in the GUI. To enable these GUI options, use the scripting function:. After successful ligand searching, one may well want to add that displayed ligand to the current model the coordinates set that provided the map mask.

Sometimes a ligand is placed more or less in the correct position, but the orientation is wrong - or at least you might want to explore other possible orientation.

To do that easily a function has been provided:. This will flip the orientation of the residue around the Eigen vector corresponding to the largest Eigen value, exploring 4 possible orientations.

As with finding ligands, you are given a choice of maps, protein masking atoms. A final selection has to be made for the cut-off level, note that this value is the number of standard deviation of the density of the map before the map has been masked. If you want to use a difference map, you must change the sigma level typically to 3 sigma otherwise you run the risk of fitting waters to difference map noise peaks.

Then the map is masked by the masking atoms and a search is made of features in the map about the electron density cut-off value. Waters are added if the feature is approximately water-sized and can make sensible hydrogen bonds to the protein atoms. Defaults are 2. The map that is marked by the protein and is searched to find the waters is written out in CCP4 format as "masked-for-waters. When Coot finds a blob, it does a crude positioning of an atom at the centre of the grid points.

It then proceeds to move to the peak of the blob by a series of translations. Often when you go to the position indicated, you can see why Coot had a problem in the refinement.

This creates a new residue at the C or N terminal extension of the residue clicked by fitting to the map. By default there are trials. It is possible that a wrong position will be selected for the terminal residue and if so, you can reject this fit and try again with Fit Terminal Residue Each of the trial positions are scored according to their fit to the map 85 and the best one selected.

If you use the Extensions Dock Sequence Sometimes, particularly with low resolution maps, the added terminal residue will wander off to somewhere inappropriate. This can be addressed in a number of ways:. Using set-pointer-atom-is-dummy 1 you can by-pass this dialog and immediately create a dummy atom at the pointer position. Use an argument of 0 to revert to using the atom type selection pop-up on a button press. They should be saved and merged with your coordinates outside of Coot.

The algorithm is straightforward. First we move to the local centre of density, then examine the density for characteristic directions and fit ideal helices of length 20 residues to these directions.

The helix is then extended if possible by checking the fit to the map of residues added in ideal helix conformation and chopped back if not. If the fit is not successful, there is instead a message added to the status bar. You can build the majority of a helical protein in a few minutes using this method you will of course have to assemble the helices and assign residue numbers and sequence later. The ideal B-form DNA is somewhat under-wound, needing 11 base-pairs to repeat instead of the expected There is no easy fix for this currently.

How is that done? There are now guis to NCS command to help you out under Extensions. However, for completeness here are the scripting versions:. If you want to copy a residue range to a specific chain, or specific list of chains rather than all NCS peer chains then make a list of the chain-ids that you wish replaced:. Note that here Coot only allows the use of datasets which has Refmac parameters set as the MTZ file was read. Optionally, you can also display the difference map. The default refmac executable is refmac5 it is presumed to be in the path.

After running refmac several times, you may find that you prefer if the new map that refmac creates after refmac refinement is the same colour as the previous one from before this refmac refinement.

If so, use:. Coot can read shelx. In the former case, coot will presume that there is a SHELX hkl file corresponding to the res file that you read in; if there is not coot will print a warning and not try to run shelxl.

In the latter case, you can specify the location of the hkl file. Coot creates a time stamped ins file and a time-stamped sym-link to the hkl file in the coot-shelxl directory. Please note that the output ins file will not be particularly useful and thus shelxl will fail if the input file was not in SHELX ins format. Sometimes one can click on a button 91 unintentionally. This button is there for such a case. It clears the expectation of an atom pick. This works not only for modelling functions, but also geometry functions such as Distance and Angle.

This is to reduce mis-clicking. This function has been provided as a precursor to functions that will as automatically as possible mutate your current coordinates to one that has the desired sequence. It will be used in automatic side-chain assignment at some stage in the future.

Coot can build missing linking regions or loops After molecular replacement, the residues of your protein could well have the correct sequence but be chopped back to CG or CB atoms.

There is a function to fill such partially-filled residues:. This identifies residues with missing atoms, then fills them and does a rotamer fit and real-space refinement. Coot will block an attempt to change the whole of a chain and the target chain id already exists in the molecule. If you use the "Residue Range" option then you can insert residues with non-conflicting residue number into pre-existing chains.

This is often useful to zero out a questionable loop before submitting for refinement. After refinement with refmac there should be relatively unbiased density in the resulting 2Fo-Fc-style and difference maps. Chi-2 for Phe, Tyr, Asp, and Glu should be between and 90 degrees.

Note that Val and Leu nomenclature errors are also corrected. The graphics follow the refinement. Often you want to move a ligand or some such from wherever it was read in to the position of interest in your molecule i. Note that this moves the atoms of the molecule - not just the view of the molecule. Maps are easily re-contoured. Maps follow the molecule. As you recentre or move about the crystal, the map quickly follows.

Unfortunately, there is a bug in map-reading. If the map is not a bona-fide CCP4 map 94 , then coot will crash. You can then choose the MTZ columns for the Fourier synthesis.

It also provides the option to apply resolution limits. This function allows Coot to read an MTZ file and make a map directly without going through the column selection procedure. You can change the column labels that Coot uses for auto-reading - here is an example of how to do that:. By default the difference map is created in auto-reading the MTZ file. There are several maps that can be generated from CIF files that contain observed Fs, calculated Fs and calculated phases:.

The first specifies the cell explicitly, and alpha, beta and gamma are specified in degrees. The second form allows the specification of resolution limits and takes the cell and symmetry from a previous molecule typically a pdb file. Maps can be re-contoured using the middle-mouse scroll-wheel buttons 4 and 5 in X Window System TM terminology.

Scrolling the mouse wheel will change the map contour level and the map it redrawn. If there is only one map displayed, then that is the map that has its contour level changed no matter what the scroll-wheel is attached to in the menu. The level of the electron density is displayed in the top right hand corner of the OpenGL canvas. If you want to tell Coot that a map is a difference map after it has been read, use:.

By default the change of the contour level is determined from the sigma of the map. You can change this in the map properties dialog or by using the scripting function:.

The default increment to the electron density depends on whether or not this is a difference map 0. To remove the limit:. By default, maps get coloured according to their molecule number. The starting colour i. The map colour gets updated as you change the value in the colour selector As subsequent maps are read, they are coloured by rotation round a colour wheel.

The default colour map step is 31 degrees. You can change this using:. For some strange reason, some crystallographers 99 like to have their difference maps coloured with red as positive and green as negative, this option is for them:. The maps need not be on the same griding, or in the same space group even. There is a scripting interface to the generation of map averages. As above, the maps need not be on the same grid or in the same space group.

The resulting map will have the same gridding and space group as the first map in the list. Typical usage:. The argument to average-map is a list of lists, each list element is a list of the map number and a weighting factor 1.

By default, the Shannon sampling factor is the conventional 1. By default, the map is re-contoured at every frame during a drag Ctrl Left-mouse. In this way, you can see electron density for big maps many unit cells and the graphics still remain rotatable. If you want to have these functions active for all maps, add the following to your initialization file Scheme :.

By default this value is 1. The skeleton is often recalculated as the screen centre changes - but not always since it can be an irritatingly slow calculation. If you want to force a regeneration of the displayed skeleton, simply centre on an atom using the middle mouse button or press the S key.

It can be educational even useful at lower resolutions to sharpen or blur a map. Pattersons can be generated using the make-and-draw-patterson function. Example usage:. If invert-mask?

This applies the rotation rotation-matrix and a translation trans to a map fragment, so that when the transformation is applied the centre of the new map is at point. Note that using a too high radius can cause overlap problems, so try with a small radius e. Alternatively, instead of typing the whole matrix, you can use a coordinates least-squares fit to generate the matrix for you. Hopefully the arguments are self explanatory ref refers to the reference molecule, of course and about-pt is a 3-number list such as is returned by rotation-centre.

You can write out a map from Coot e. The validation functions are still being added to from time to time. In future there will be more functions, particularly those that will interface to other programs.

When you edit the molecule i. When you mouse over a representation of a residue a little square or triangle the residue label pops up. In the Ramachandran plot window, the current residue is highlighted by a green square. A restraints-based geometry analysis of the molecule. The distortion is weighted by atom occupancy. The distortion of the geometry due to links is shared between the contributing residues.

A clickable list is created of atoms whose chiral volume in the model is of a different sign to that in the dictionary. During refinement and regularization, Coot will pop-up dialogs warning about chiral volume errors - if you have them. This can be annoying You can inhibit this dialog like this:. Usually you can pull the CA to the other side of the plane made by the chiral neighbouring atoms using ctrl left-click.

Sometimes giving the CB a good old tweak is the easier way. This is an interface to the Blobs dialog. A map and a set of coordinates that model the protein are required. A blob is region of relatively high residual election density that cannot be explained by a simple water. So, for example, sulfates, ligands, mis-placed sidechains or unbuilt terminal residues might appear as blobs.

The blobs are in order, the biggest at the top. This is one of the fastest ways to validate a model and its data presuming that the difference map comes from a post-refinement mFo-DFc map. It highlights regions where the model and the data do not agree. Lesser peaks within a certain distance by default, 2. This cuts down on the number of times one is navigated to a particular region because of ripple or other noise peaks around a central peak. Sometimes waters can be misplaced - taking the place of sidechains or ligands or crystallization agents such as phosphate for example In such cases the variance of the difference map can be used to identify these problems.

This function is also useful to check anomalous maps. Often waters are placed in density that is really a something else, perhaps a cation, anion, sulphate or a ligand. If such an atom diffracts anomalously this can be identified and corrected.

By default the waters with a map variance greater than 3. One can be more rigorous by using a lower cut-off:. This difference map must have been calculated using the waters. You will need to run Refmac or some other refinement first first The molprobity tools probe and reduce have been interfaced into Coot currently, the interface is not as slick as it might be.

However, the tools are useful and can be used in the following way:. A new molecule with Hydrogens is created by reduce and read in. To get a semi-static view dots are regenerated in the region of zone after a "Real Space Refinement" :. However, we can use properly refined temperature factors to detect outliers.

We take the Z value as half the difference between the B-factor of the NE2 and OE1 divided by the standard deviation of the B-factors of the rest of the residue.

Coot provides several graphs that are useful for model validation on a residue by residue basis : residue density fit, geometry distortion, temperature factor variance, peptide distortion and rotamer analysis.

The density fit graph shows the density fit for residues. The score is the average electron density level at the atom centres of the atoms in the residue.

The height of the blocks is inversely proportional to the density average. The residue density fit is by default scaled to a map that is calculated on the absolute scale. Sometimes you might be using a map with density levels considerably different to this, which makes the residue density fit graph less useful.

To correct for this you can use the scripting function:. Residue rotamers are scored according to the prior likelihood. Note that when CD1 and CD2 of a PHE residue are exchanged simply a nomenclature error this can lead to large red blocks in the graph apparently due to very unlikely rotamers. There are several other residues that can have nomenclature errors like this. To fix these problems use. But not too much.

Anything more than 13 degrees is suspicicous. Unexpected peptide bonds show up red by default. If cis peptides are to be expected, and should not marked as bad, then you can tell this to Coot using:. Up: Representation [ Contents ][ Index ]. However, partial charges are only used under certain conditions. If partial charges are not used, then the fall-back is to use charges from side-chains charged at physiological pH Arg, Lys, Asp, Glu. The results are returned as a web page in web browser.

The browser type can be specified as in this example:. Building structures using low resolution data is a pain. We hope to make it less of a pain in future, but there are some things that you can do now. Everything except the 0-coot. You can stop the state and history files being written if you start coot with the --no-guano option. Coot will occasionally ask you to clear up the coot-backup directory.

You can adjust the behaviour in a number of ways:. So, if you wanted to clear out everything more than 1 day old, every time, without Coot asking you about it:. If you get stuck in "translate" mode in the GL canvas i. Note that left-mouse in the graphics window is used for both atom picking and rotating the view, so try not to click over an atom when trying to rotate the view when in atom selection mode. However, these parameters can be tweaked so that slower computers perform better:.

Up: Other Programs [ Contents ][ Index ]. This is available so that the scripting functions know whether on not to put themselves onto in as menu items. We should clean up this rather obscure interface at some stage. Returns: zero on success, or -1 if an error occurred. If dir already exists as a directory, return 0 of course. Next: remove-dictionary-glob-extension , Previous: remove-coordinates-glob-extension , Up: File System Functions [ Contents ][ Index ].

Up: Widget Utilities [ Contents ][ Index ]. This is a raw interface function, you should generally not use this, but instead use is-solvent-chain? Returns: -1 on error, 0 for no, 1 for is "a solvent chain". This is a raw interface function, you should generally not use this, but instead use is-protein-chain? Returns: -1 on error, 0 for no, 1 for is "a protein chain". This is a raw interface function, you should generally not use this, but instead use is-nucleicacid-chain? Returns: -1 on error, 0 for no, 1 for is "a nucleicacid chain".

I am not dogmatic about it. Yep, hundreds of functions are made available to the user via SWIG and can be scripted in either Python or scheme. Yes, it is a bit. Binary distributions for a selection of systems are built every night. There is an "autobuilder" build script which we use to make build the binaries. You can get WinCoot here. Please see the Coot FAQ.

Will you ever release version 1.