Coot Scripting

1. Cool Scripts Roblox Pastebin
2. Cool Scripts Roblox
3. Coot Python Scripting
4. Coot Scripting For Beginners

Print the Builder Support page, check off what you want, and enclose US funds to order the Coot plans, newsletter or any of 3 books, called The Coot Story, The Coot in a Nutshell and The Essential Coot. Richard Steeves, Editor. The Coot-builder's Newsletter. 6958 Applewood Drive. Madison, WI 53719, USA. Phone: 608/833-5586. Coots are medium-sized water birds that are members of the rail family, Rallidae.They constitute the genus Fulica, the name being the Latin term for 'coot'. Coots have predominantly black plumage, and—unlike many rails—they are usually easy to see, often swimming in open water. Coot seems to be able to figure out missing regions. However for one example it was crucial to specify at least the correct equivalent residues at the N-terminus and a deletion and missing residues at the C-terminus were detected correctly. Coot is a molecular-graphics application for model building and validation of biological macromolecules. A wrapper shell script called 'coot' will reside in /usr/local/bin/coot when you are done. 10.11: Go to the Stand-alone Coot for 10.11 page for a 10.11-specific version, 64-bit. Latest Automated Nightly Build OS X installer packages for 10.13 and newer.

For the usual Coot problems and bugs have a look at Paul's FAQ page. Often RTFM helps too, therefore the Coot documentation, tutorial etc. is provided for your comfort. Nevertheless, WinCoot might crash on you unexpectedly (like a lot of other Windows programs...). Please let me know if there is any further bugs rather than the following and please don't tell me about these ones again.

• Installation and Windows problems
  • WinCoot on Windows 7 (and later)
  • Does stereo work with WinCoot?
• Using WinCoot
• Old FAQs (deprecated, pre-0.3, etc.)

(Win)Cootreference, citation and furtherinformation

The official reference for WinCoot is published now:

You can use this BibTeX database entry (which can be imported into EndNote or directly download the file for import in your citation manager to your citation manager)... format as you please:

The Coot paper is published in the proceedings of the 2009 CCP4 Study Weekend.

You can view and download the paper from here:

Additional information on Coot especially WinCoot can be found in the CCP4 Newsletter (Number 42, Summer 2005). Feel free to cite it as well as the 'official' Coot reference in case WinCoot was useful for you.
Lohkamp, B., Emsley, P. & Cowtan, K. (2005) Coot News. CCP4 Newsletter, 42, Contribution 7.

Installation and Windows problems

Which Windows version does WinCoot run on?

WinCoot has been successfully tested on Windows 10, Windows 8(.1), Windows 7, Windows Vista, Windows XP, Win2000, and WinNT . There may be some specific problems...

WinCoot on Vista

WinCoot in general works on Vista. As of 0.5-pre-1 (1339) WinCoot should work properly with Desktop Compositing (Vista Theme) as you can see here.
However, if you have problems with compositing, here are some solutions to overcome this problem:

1. disable the desktop compositing of coot-real.exe (e.g. in C:WinCootbin) or wincoot.bat (e.g. in C:WinCoot; prior to 0.8.8 runwincoot.bat). [Right-Click coot-real(.exe)->Properties->Compatibility->Disable desktop composition]
2. set the theme to Windows Classic. [Control Panel->Appearance and Personalization->Pernsonalization/Change Theme->Windows Classic]
3. in your graphics card Control Panel switch off any threading option.

WARNING:: There may be other problems on Vista.

WinCoot on Windows 7 (and later)

Initial reports suggest that WinCoot works fine on Windows 7 and 8. If you have problems please report to me (incl. details such as graphics card, processor, etc) and try the suggestions for Vista. More news once I tested more myself.

Problem resizing/maximizing or updating the WinCoot window.

WinCoot may not update the graphics window upon resize/maximize (something like this) or in general not update (like this). The reason is most likely a graphics card driver issue. It usually can be fixed by installing an updated and appropriate graphics card driver from the manufacturer. E.g. if you have a 'proper'/dedicated graphics card (i.e. NVIDIA, ATI etc; not a build-in Intel) it is recommended to install the drivers from the manufacturer rather than the ones supplied by Windows.

Dll errors such as 'Can't find entry point bla in xyz.dll':

This is related to Windows picking up wrong dll versions. Either download a new installer (after WinCoot 0.8.8) or do the following:
Copy (or move) everything (files and folders) from:
C:YourWinCootDirectorylibexec
to
C:YourWinCootDirectorybin

Downloading of pdbs does not work/Python errors

This is related to Windows picking up the wrong version of Python. Either download a new installer (after WinCoot 0.8.1) or do the following:
Copy (or move) the file python27.dll from:
C:YourWinCootDirectorybin
to
C:YourWinCootDirectorylibexec

Installer hangs

In the end of the installation the Installer may become unresponsive (only seen on Windows 8 and above so far). It appears that (usually) WinCoot is installed correctly though and there is no reason for concern. Just kill the Installer. Working on a fix is in progress.

Display is not responsive in full screen mode

This may be caused by the auto-hide function of the Windows Taskbar. If you disable the auto-hide Taskbar WinCoot should work fine. [Thanks to Jack Sadowsky]. On other occasions it was actually the other way around (enabling the auto-hide function) which works.
Another possible fix (untested) may be to use WinCoot's full screen mode (feedback appreciated...):

• right mouse click on main toolbar (besides the Go To Ligand icon)
• 'Manage Buttons'
• Select 'Full Screen' under Display
• (De)Activate full screen mode using the new button

WinCoot hangs opening and/or saving files

This may be caused by the modern file chooser. So, either revert to the classic one (Edit->Preferences...->General/File Selection tab; top pane change to Classic File Selector) or avoid using the GUI for file selections by using e.g. drag'n'drop to open files and Quick Save (Ctrl s) for saving files.

WinCoot 'automatically' loads pdb files repeatedly

This is most likely cause by other software interfering with WinCoot. The best known (to me) is the English-Chinese dictionary software called 'youdao'. So, either close the offending program or in the case of 'youdao' just close the function of automatic translation when select or mouse move. In this way you can even use WinCoot and 'youdao' together.

WinCoot does not start/crashes immediately

This could be caused by other software interfering with WinCoot; one know example is 'Duet Display' (thanks André Graça). Uninstalling the offending software will of course help, but may not be desired. Maybe temporarily disabling running services of the other software may help.
If this is not the case and/or solving the problem, please get in touch.

Problems with virtual desktops (e.g. Dexpot, VirtuaWin)

Nothing which can be done from WinCoot side (*). However, you can fix this by showing WinCoot on all Desktops. Here a thread about this topic on the bb.
(*) For the more interested. It appears that gtkglext does not work well with newer versions of GTK which causes this to be problematic recently now.

Ramachandran plot (or sequence view) crashes

Fixed in 0.8.9 pre-releases (from 7109 onward), so please download the latest installer.
This is caused by some underlying graphics libraries and usually happens with larger files. There is a fix in the pipeline but sadly no news as to when it will be available. In the meantime I can only suggest to split your larger structure into smaller ones (e.g. chains) and/or use this script to get at least a clickable list of outliers. [Then run the script file (Calculate->Run script), which will give a new menu under validate to give you outliers in a button list form. NB if you put the file in your .coot-preference directory it will always be loaded.]

Bizarre connectivity of coordinate files

I guess you see something like this. This should not happen any more (from 0.3.3.1), however there is rare cases on Windows 7 where it occurs again (this is progress for you!). Actually it happens randomlly on Windows 10 as well (usually after merging of molecules). So if it does please let me know about your system and try the following:
It may be that you have a 'non-english speaking' computer and changing some settings on your computer may fix this.
Go to Start -> Settings -> Control Panel -> Regional and Language Options. Then Customise your settings and change your Decimal symbol to '.' (dot) [was a ',' comma I guess]. In turn you might want to change you Digit grouping symbol from '.' (dot) to ',' (comma) to avoid possible confusions. This is the procedure for 'British' Windows XP, but should be similar on other Windows systems and/or languages.
In a more permanent fix (without messing with your usual setting) you can try the following:

• download the language setting files.
• unzip the files in yourWinCootDirectory
• Edit your wincoot.bat (runwincoot.bat prior to 0.8.8) file the following way:
• place the following after set COOT_PREFIX=C:WinCoot

• place the following at the end of the file:

• N.B. the lang_xxx.xml files are for Swedish Swedish (sv-SV) and you have to change them to your regional setting (for codes see this MS site).
  

WinCoot installer warnings

You may get a Windows warning that the installation of WinCoot could not be completed for some reason. In most cases this is caused by an incomplete download of the installer. Please make sure that the WinCoot installer is downloaded completely. If not, try again. A brief check about the size can help (something above 70Mb currently). The correct way is to varify the download via the md5sum (stable, development).

I only get a grey display window

Turning down your graphics card acceleration should solve this. To do so go to Start->Settings->Control Panel->Display->Settings->Advanced->Troubleshoot. Then move the slider to towards None (usually one bar above None is still acceptable). This is most likely due to graphics card/drivers. Currently I don't know how to fix it otherwise.

Does stereo work with WinCoot?

Yes, it works fine. All of it, hardware, side-by-side, Zalman, 120Hz LCD, ... IF you have the right hardware!!

WinCoot with NVIDIA 3D Vision/120Hz LCDs?

This works if you have the high end Quadro graphics cards which enable OpenGL. To set the graphics card up, please follow the instructions e.g. given by the PyMOL community. You find general information here and here are specific instruction for Vista and XP.

WinCoot with NVIDIA and Win 10?

If you run into problems with stereo on Windows 10 (using an NVIDA card), you can try the following (thanks to Jose Brito):

• Open NVIDIA Control Panel --> Manage 3D settings.
• Go to Program Settings tab.
• Add the file you launch the program from by clicking on Add button.
• In the setting window, change the 'Power Management Mode' to 'Prefer Maximum Performance'. Also below settings as well:
• Vertical sync - off
• Threaded optimization - off
• Triple buffering - off
• Stereo enable on
• Run the program and check.

Others (Kent Rossman) have reported that some XBOX servive (GameDVR) may intefer with the stereo. Disabling and uninstalling this may help.

There may be other issues though which are related to the fact that WinCoot is 32bit and some graphics card drivers don't seem work well with 32bit applications. The hope is that this will go away with 64bit WinCoot (in beta release but packing issues at the moment). First test, however, seem not too promising. Maybe related to one of above.

Text missing in some widgets when using Scheme/Guile scripting

Currently Scheme/Guile is not available, so no problem there...

Using WinCoot

What about WinCoot and CCP4?

Coot is part of the CCP4 Windows package (6.0.x) now. Previously it was CCP4's own version and didn't seem to be fully functional (it wasnt done by me). Now CCP4 is distributing my WinCoot, so all is fine.
However, I don't know when updates for the CCP4 packages will be made available and how it interplays with CCP4i2!

How do I change the font size of the labels?

You can edit your cootrc file (found in C:YourWinCootDirectorysharecoot).
Please replace the line (under style 'defaultfont'; line ~26)
font = '-adobe-helvetica-medium-r-normal--*-75-*-*-*-*-*-*,*'
with (e.g.)
font_name = 'tahoma 12'
You can choose other (available) font names there too as well as further increase (or decrease) the size of the label (default size is 8).

What are these 'Generic objects'?

Generic objects are other displayed objects than models or maps, e.g. probe dots.These are (dot) objects generated by the programs probe and reduce from the Richardson Lab. The generic objects will show you intra-molecular interactions. You will need to install these programs to use this function in (Win)Coot. You can download them from here. Ideally put the executables (probe.exe and reduceV2.13.2.win.exe) somewhere in you PATH ([or] e.g. in C:YourWinCootDirectorybin) and off you go. More detailed instructions below.

How do I get MolProbity (probe and reduce) working in WinCoot?

Now you can get probe and reduce together with WinCoot (select during the installation). Or you can use the programs which come with CCP4 (if they are found in the PATH).
For older WinCoot versions without probe and reduce, depending on your WinCoot version follow these steps:
WinCoot 0.5.1(-pre-1) and later:

1. download probe. (or look here; 2.12.x)
2. download reduce. (or look here; 3.13.x)
3. for probe:
• unzip probe*.exe.zip
• rename/copy probe*.exe to probe.exe
• copy/move probe.exe into YourWinCootDirectorybin(orsomewhereelseinyour PATH ; for an alternative see 5)
4. for reduce:
   
• extract reduce*.zip
• rename/copy reduce*.exe to reduce.exe
• copy/move reduce.exe into YourWinCootDirectorybin(orsomewhereelseinyour PATH ; for an alternative see 5)
• Optionally: copy/move reduce_wwPDB_het_dict.txt to the same directory where you moved reduce.exe to

5. OPTIONAL ALTERNATIVE: if the executables are NOT in PATH (e.g. YourWinCootDirectorybin): edit either group_settings.py (found in YourWinCootDirectorysharecootpython)sothatprobe_commandandreduce_command describe the location of your files (e.g. probe_command = 'C:Mydirectoryprobe.exe') OR add the following lines to e.g. YourWinCootDirectory.coot.py:
• probe_command = 'C:Mydirectoryprobe.exe'
• reduce_command = 'C:Mydirectoryreduce.exe'

WinCoot 0.5:

1. as for WinCoot 0.5.1 BUT observe that the 'Molprobity Probe Clash Gaps' GUI is not working properly!

Older version that 0.5:

1. download probe. (or look here BUT DO NOT INSTALL PROBE NEWER THAN 2.11 - for now)
2. download reduce. (or look here)
3. run probe*.exe and extract into YourWinCootDirectorybin (or somewhere else in your PATH ; for an alternative see 5)
4. extract the content of reduce*.exe.zip and move the files from reduce4win into YourWinCootDirectorybin (or somewhere else in your PATH ; for an alternative see 5)
5. if the executables are not in PATH : edit group_settings.py (found in YourWinCootDirectorysharecootpython)sothatprobe_commandandreduce_command describe the location of your files (e.g. probe_command = 'C:Mydirectoryprobe.exe')

Done!

How do I get raster3d and/or povray working with WinCoot?

Just download and install the appropriate program (raster3d, povray) and WinCoot should find them. However it might be better (faster) to put them somewhere in your PATH.

How do I handle different projects?

When working on different projects you might like to go back to these different ones when running WinCoot, i.e. reading in a 0-coot-state.py file for each project. Since the coot state file is always loaded from the directory which WinCoot is started from you have to change this. You can do this by having different WinCoot shortcuts running in different directories or by starting WinCoot (wincoot.bat; runwincoot.bat prior to 0.8.8) from the Command Prompt in the appropriate directory. Alternatively make a copy the 0-coot-state.py files and read it in as a python script file. Some additional information can be found on the installation page.

How does Python scripting work?

Python scripting is different to (default) guile scripting which is mainly described in Paul's instructions (although it's mentioned somewhere, fairly hidden). You have to change the commands in the following way:
Some more information on Scheme/Guile and Python scripting can be found on the Coot WIKI page.

How do I use extra parameters in the Refmac interface?

If you have CCP4 installed on your computer you should be able to run REFMAC5 on your build structure from WinCoot. Be aware that there is some slight changes to the handling and filenames for extra refmac parameters in comparison to 'normal' Coot. First the file which give refmac extra parameters is called refmac-extra-params.txt for easy text editing (see an example here). It is a simple text file which can include all your refmac extra parameters in a new line (for an example see here). WinCoot will search for the file in the directory from where WinCoot is started from. Refmac extra parameters can be given in 3 different locations (the highest priority first), in your .coot.py file, in the refmac.py and in the refmac-extra-params.txt file (in $COOT_PYTHON_DIR). The first 2 require 2 lines in the code like:

Other WinCoot information

Old FAQs (deprecated, pre-0.3, etc.)

GTK/GDK/Pango warnings

You may see some GTK, GDK and/or Pango warnings in the Command Prompt Windows (some will be there on start-up, but otherwise I haven't seen it for a while). Please ignore these warnings as long as WinCoot doesn't crash. If it does, please let me know.

Crash on reading mtz files

On some computers WinCoot crashes when opening mtz files. However, this should be fixed now, I hope!
If it happens too often and is too painful then the easiest way to avoid it is to read in map files. Otherwise try reading in the mtz file again (and again...). Sometimes using a script or state file seems to help as well.

Hardware-Stereo

Cool Scripts Roblox Pastebin

There has been several reports that stereo is fairly unstable. However this should be fixed now and no extra version needs to be downloaded.

Others

• On some computers there seem to be a conflict of WinCoot with CCP4i due to the SYMINFO variable (only beta2). This should not occur any more since we use a .bat file to run WinCoot now...

Cool Scripts Roblox

Coot Python Scripting

Coot Scripting For Beginners