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Coot

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[[Image:Coot-with-ATP-vector.png|400px25%|thumb|right]]
Coot is a graphics program for building, refining and analysing macromolecular models obtained with crystallographic procedures.
There is a [http://wwwwww2.biopmrc-lmb.oxcam.ac.uk/Personal/pemsley/coot/ homepage] with extensive [http://wwwwww2.biopmrc-lmb.oxcam.ac.uk/Personal/pemsley/coot/web/docs.html / documentation]. The program may be downloaded for Linux, Mac and Windows computers from the [http://wwwwww2.ysblmrc-lmb.yorkcam.ac.uk/~emsley/software/binaries/ primary server] (as of July 10, 2009 there's a new site at http:/Personal/www.biop.ox.ac.ukpemsley/coot/devel/build-info.html) or, if that is not available, from an [ftp:binaries//turn5.biologie.unipre-konstanz.derelease/coot external mirrorprimary server]. The license of Coot is GNU GPL.
=Installing Coot=
==Installing Coot on OS X==
 
OS X install packages for nightly builds that work on 10.8.X and 10.9.X are available here: [http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot Coot OS X package installers]
 
Please refer to the [http://sage.ucsc.edu/xtal/wiki/index.php/Installing_Coot_on_OS_X Installing Coot on OS X] page
==== Example: installing a 64bit nightly CentOS5 binary build on 64bit SL6.1 ====
First of all, SL (Scientific Linux) is a derivative of RHEL, as is CentOS. So all three OSs behave exactly the same.
The binaries with "x86_64" binaries are for 64bit systems; the "i386" binaries are for 32bit systems. Since my notebook is 64bits ("uname -a" reports "x86_64" more than once), I download ftp://turn5.biologie.uni-konstanz.de/coot/software/binaries/nightlies/pre-release/coot-0.7-pre-1-revision-3999-binary-Linux-x86_64-centos-5-python-gtk2.tar.gz (the main server is slow, so I use the mirror). As root, I "cd /usr/local/src" and un-tar. Next, have to find out which libraries are missing. This can be achieved by (''note the use of LD_LIBRARY_PATH in the second command - do not permanently modify LD_LIBRARY_PATH !''):
[root@localhost]# cd coot-Linux-x86_64-centos-5-gtk2-python
[root@localhost]# LD_LIBRARY_PATH=lib ldd bin/coot-real | grep found
: So the answer is: there is /usr/lib64/libssl.so which is at version 10, which is compatible with the version we need (6). For libcrypto.so the same is true. So just
cd cd coot-Linux-x86_64-centos-5-gtk2-python/lib/
ln -s /usr/lib64/libssl.so libssl.so.6
ln -s /usr/lib64/libcrypto.so libcrypto.so.6
: The way these symlinks are made they would even work if RHEL upgrades libssl or libcrypto to higher versions. Works for me.
Final step(this does not need to be repeated for a new coot version): create /usr/local/bin/coot with
#!/bin/csh -f
setenv LANG C
and make it executable with
chmod a+x /usr/local/bin/coot
 
=== Installation on Debian/Ubuntu from debian archive files ===
As an alternative, you might wish to exploit the debain dpkg/apt/synaptic package management system on Ubuntu and other Debian linux distributions using (unofficial)
[http://diablo.ucsc.edu/~wgscott/debian/coot_hardy/ pre-compiled debian packages for coot and its dependencies]. (These will be discontinued when official packages become available.)
 
To do so, simply download the deb files and install with the command
 
sudo dpkg -i *.deb
 
dpkg will complain if a dependency is missing rather than install a broken program.
 
=== Packages for Ubuntu ===
 
A pre-packaged version of Coot (0.7-pre-1) for Ubuntu is available from mok0's Personal Package Archive (PPA) on Launchpad. Currently, packages for Ubuntu 10.04 (Lucid) and 10.10 (Maverick) are available.
 
To install the coot package on your system, you first need to install the public key for mok0's PPA:
 
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 1DC81A57
 
Next, add the PPA repository to your /etc/apt/sources.list file:
 
sudo add-apt-repository ppa:mok0/ppa
 
That's it! Now, you should be able to:
 
apt-get update && apt-get install coot
 
This version of Coot only supports the Python scripting language.
 
=== Mandriva Installation ===
 
To install the coot on Mandriva 2010.0 use the ubuntu distribution:
tar zxf coot-0.6.2-binary-Linux-i686-ubuntu-8.04.1-python-gtk2.tar.gz
 
in the .cshrc file:
alias coot 'source /prog/CCP4/ccp4-6.1.13/include/ccp4.setup-csh ; /prog/coot-Linux-i686-ubuntu-8.04.1-gtk2-python/bin/coot'
 
 
=== Converting to rpm packages ===
You can convert any debian package file into an rpm file using the program ''alien''. I have done this and have made the [http://diablo.ucsc.edu/~wgscott/debian/rpm/coot/ resulting packages] available.
=== Installation from source code via autobuild scripts ===
===Controls===
[[Image:Coot-controls-small.png|200px]]
Note that the stereo effect is very sensitive to the vertical position of your eyes relative to the screen: if you don't see stereo, try tilting the screen.
 
=== Stereo: left/right (and front/back) interchanged? ===
 
Establish an additional toolbutton "swap stereo":
 
Main Toolbar -> right mouse click-> Manage buttons-> select Swap Stereo
 
Or for the script minded:
 
switch_stereo_sides()
 
This will toggle the stereo images left and right.
===External Links===
[[yellowify_molecule_keys.py]]
 
===Example 3: NCS Rotamer differences===
 
To show NCS where NCS-related side-chains have different rotamers:
 
[[ncs_rotamer_differences.py]]
 
===Example 4: Morphing GUI===
 
GUI to easily access jiggle fit and morphing (currently pre-release Coot required, may be moved into trunk):
 
[[morph_residues_gui.py]]
 
===Example 5: Ensemble GUI===
 
GUI to allow navigation through structural ensembles as obtained e.g. from ensemble refinement:
 
[[ensemble_plugin.py]]
==Python to Scheme and return==
Here some simple rules how to translate from Scheme to Python. To translate the other way around, i.e. Python to Scheme, just turn the rules around:
# replace Replace all '-' with '_' (except in equation when you need arithmetic '-' minus signs)# move Move the brackets around the argument(s)# separate Separate multiple arguments by commas rather than spaces# replace Replace 'define' for functions with 'def' for functions and for assignments with an '='for assignments
# Make sure to use indentation for the function content [Python is indentation sensitive] and a ':' after the function definition.
A: Join the [[Coot Janitors]] project. This is a project to get new people involved in improving Coot, by acting as a clearing house for simple tasks which need doing, and providing documentation for doing them.
 
 
== Get rid of the "fix nomenclature" check ==
Q: Is it possible to deactivate the nomenclature errors check? Sometimes this check is not very useful and it becomes rather annoying when one has several molecules loaded only wants to look at the structures...
 
A: Add to your ~/.coot or whatever:
(set-nomenclature-errors-on-read "ignore")
A: Yes this fails. Hydrogens are named differently to SHELX hydrogens. In principal this could be made to work if the dictionary was reworked to use SHELX hydrogen names. This would also fix the chi angles problem too of course.
 
Specific Q3: I am unable to open the output pdb file from ShelXL in Coot.
 
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 .res file rather than the pdb, then the subsequent .ins file contains lots of "header" information.
 
Another answer to questions 1+2 is to rename the hydrogen atoms in the shelxl res-file to match the mmCIF dictionaries used by Coot. This only needs to be done once as shelxl does not modify these names. Except for a few manual editions, the renaming can be done semi-automatically using regular expressions (replacing A->1, B->2, etc).
 
Concerning question 3, the Coot -> Extensions -> Module -> SHELXL menu entry works really well now. It reads in all relevant shelxl files and provides a menu highlighting the problematic areas in the model.
==Image quality on NVidia cards==
A: there are 2 loop fitting tools in Coot
# C alpha -> Mainchain [http://www2.mrc-lmb.bioch.oxcam.ac.uk/personal/pemsley/coot/docweb/docs/coot.html#C_002dalpha-_002d_003e-Mainchain],[http://www2.mrc-lmb.bioch.oxcam.ac.uk/personal/pemsley/coot/docweb/docs/coot.html#Building-Links-and-Loops]# DB Loop: (No good documentation) [http://www2.mrc-lmb.bioch.oxcam.ac.uk/personal/pemsley/coot/docweb/docs/coot/protein_002ddb_002dloops.html#protein_002ddb_002dloops] Extensions -> Modelling -> DB Loop...
==LSQ superpositions==
(add-key-binding "Dynamic LSQ overlay" "Y" dynamic-lsq-match)
 
== reading MTZ file with experimental PHI and FOM using --auto ==
 
Q: There is the --auto <filename> commandline option for auto-reading mtz files (mtz file has the default labels FWT, PHWT). Can this be made to work with a SHELXE .phs output file after converting with convert2mtz ? - the resulting MTZ file has labels F PHI FOM.
 
A: use: coot --python -c 'make_and_draw_map("sad.mtz", "F", "PHI", "FOM", "/HKL_base/HKL_base/FOM",1, 0)'
 
== NCS Rotamer differences ==
 
Show me where NCS-related side-chains have different rotamers
 
(define (compare-ncs-rotamer imol chain-A chain-B)
(let ((n-residues (chain-n-residues chain-A imol))
(mismatched-rotamers '()))
(for-each
(lambda (serial-number)
(let ((res-name-A (resname-from-serial-number imol chain-A serial-number))
(res-no-A (seqnum-from-serial-number imol chain-A serial-number))
(ins-code-A (insertion-code-from-serial-number imol chain-A serial-number))
(res-name-B (resname-from-serial-number imol chain-A serial-number))
(res-no-B (seqnum-from-serial-number imol chain-A serial-number))
(ins-code-B (insertion-code-from-serial-number imol chain-A serial-number)))
(if (not (= res-no-A res-no-B))
(begin
(format #t "sequence number for ~s do not match~%" res-no-A))
(if (not (string=? res-name-A res-name-B))
(begin
(format #t "residue names for ~s do not match~%" res-no-A))
(let ((rot-name-A (get-rotamer-name imol chain-A res-no-A ins-code-A))
(rot-name-B (get-rotamer-name imol chain-B res-no-B ins-code-B)))
(if (not (string=? rot-name-A rot-name-B))
(begin
(set! mismatched-rotamers
(cons (list imol chain-A res-no-A ins-code-A
res-name-A
(if (string=? rot-name-A "") "-" rot-name-A)
(if (string=? rot-name-B "") "-" rot-name-B))
mismatched-rotamers))))
)))))
(range n-residues))
(dialog-box-of-buttons "Mismatched Rotamers"
(cons 300 300)
(map (lambda(rotamer)
(let ((label (string-append " "
(list-ref rotamer 1)
" "
(number->string (list-ref rotamer 2))
(list-ref rotamer 3)
" "
(list-ref rotamer 4) ;; res-name
": "
(list-ref rotamer 5)
" vs. "
(list-ref rotamer 6)))
(thunk (lambda ()
(set-go-to-atom-molecule imol)
(set-go-to-atom-chain-residue-atom-name
(list-ref rotamer 1)
(list-ref rotamer 2) " CA "))))
(list label thunk)))
mismatched-rotamers)
" Close ")))
 
 
 
And one would use this something like:
 
;; example usage:
(let ((imol (read-pdb "test.pdb")))
(compare-ncs-rotamer imol "A" "B"))
 
== make RSR in coot 0.8.1 behave like in earlier versions ==
 
Q: We've noticed a new behavior in real space refinement in coot 0.8.1 whereby dragged atoms are more tightly restrained to their initial positions than in earlier versions. This seems to be described in the release notes by:
 
o BUG-FIX: The amount that the other atoms ove with moving the picked atom has been reduced (but is configurable)
 
A: Add e.g. this to your ~/.coot.py file:
 
set_refinement_drag_elasticity(0.8)
 
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: Because of cis-peptides. My worry was that in the previous regime, it was
too easy to introduce cis-peptides when fitting to low resolution maps.
I believe the current default setting is much less likely to do that.
 
Q: I've tried various settings of refinement_drag_elasticity and I need to lower it to 0.5 or so before any semblance of earlier behavior appears.
 
A: It used to be 0.167, I think.
 
== Molprobity not active in COOT ==
 
Q: I am using COOT 0.8.1 EL that comes with the CCP4 6.5.010 on my Mac OS X 10.10.2. I wanted to run molprobity but the Validate > Probe clashes button in my pull down menu is not active. Is this function available in this COOT version?
 
A: Reduce and probe are separate programs available from the Richardson’s lab at Duke http://kinemage.biochem.duke.edu/. Download and install on your box. Then coot needs to be told in some instances where it can find these executables. I have the following lines in my ~/.coot file in Linux.
 
<pre>
;; .coot
;; This file is required. As of coot 0.8pre no other mechanism for
;; enabling probe in coot works
;;
;; This is full pathname of molprobity's probe program
(define *probe-command* "/apps/xray/bin/probe")
;; This is full pathname of molprobity's reduce program
(define *reduce-command* "/apps/xray/bin/reduce")
</pre>
Untried: if you have Phenix installed: it comes with phenix.probe and phenix.reduce - you could insert the paths to these binaries into the above definitions.
 
== some symmetry mates not shown ==
 
Q: This structure has been solved and refined using phenix in the hexagonal setting of space group R 3. There is one copy per asymmetric unit in R 3. As you can see from the attached image, coot is rendering some but not all of the symmetry mates.
 
A: Turn up the radius a bit and use (set-symmetry-shift-search-size 3) . I would have thought that 2 is big enough, but maybe not in this case.

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