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Coot

1,706 bytes added, 07:14, 10 September 2019
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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.
==== 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
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]]
[[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==
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: 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==
(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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