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Coot: Difference between revisions
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[[Image:Coot-with-ATP-vector.png| | [[Image:Coot-with-ATP-vector.png|25%|thumb|right]] | ||
Coot is a graphics program for building, refining and analysing macromolecular models obtained with crystallographic procedures. | Coot is a graphics program for building, refining and analysing macromolecular models obtained with crystallographic procedures. | ||
There is a [http:// | There is a [http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/ homepage] with extensive [http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/ documentation]. The program may be downloaded for Linux and Windows computers from the [http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/pre-release/ primary server]. The license of Coot is GNU GPL. | ||
=Installing Coot= | =Installing Coot= | ||
==Installing Coot on OS X== | ==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 | Please refer to the [http://sage.ucsc.edu/xtal/wiki/index.php/Installing_Coot_on_OS_X Installing Coot on OS X] page | ||
==Installing Coot on Windows== | ==Installing Coot on Windows== | ||
Please refer to | Please refer to [https://github.com/bernhardcl/coot/releases Bernhard Lohkamp's WinCoot download] page. | ||
==Installing Coot on Linux== | ==Installing Coot on Linux== | ||
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This is the recommended way for those who do not want to delve into the mysteries of compiling and linking a great but complex piece of software. Read the (somewhat outdated, it seems) [http://www.ysbl.york.ac.uk/%7Eemsley/coot/coot-faq.html Coot FAQ] to find "Additional Notes" for your operating system. | This is the recommended way for those who do not want to delve into the mysteries of compiling and linking a great but complex piece of software. Read the (somewhat outdated, it seems) [http://www.ysbl.york.ac.uk/%7Eemsley/coot/coot-faq.html Coot FAQ] to find "Additional Notes" for your operating system. | ||
In short, just go to http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ | In short, just go to http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ and pick a suitable binary, e.g. | ||
coot-0.5-pre-1-revision-1003-binary-Linux-i386-fedora-5.tar.gz for a Red Hat Enterprise Linux 5 or CentOS-5 system (Fedora 6 corresponds to RHEL5, thus Fedora 5 binaries are OK). If you prefer a "stable" binary, these are at http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable/. | coot-0.5-pre-1-revision-1003-binary-Linux-i386-fedora-5.tar.gz for a Red Hat Enterprise Linux 5 or CentOS-5 system (Fedora 6 corresponds to RHEL5, thus Fedora 5 binaries are OK). If you prefer a "stable" binary, these are at http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable/. | ||
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==== Example: installing a 64bit nightly CentOS5 binary build on 64bit SL6.1 ==== | ==== 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. | 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 | 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 coot-0.7-pre-1-revision-3999-binary-Linux-x86_64-centos-5-python-gtk2.tar.gz. 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]# cd coot-Linux-x86_64-centos-5-gtk2-python | ||
[root@localhost]# LD_LIBRARY_PATH=lib ldd bin/coot-real | grep found | [root@localhost]# LD_LIBRARY_PATH=lib ldd bin/coot-real | grep found | ||
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and make it executable with | and make it executable with | ||
chmod a+x /usr/local/bin/coot | chmod a+x /usr/local/bin/coot | ||
=== Installation from source code via autobuild scripts === | === Installation from source code via autobuild scripts === | ||
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===Controls=== | ===Controls=== | ||
[[Image:Coot-controls-small.png | [[Image:Coot-controls-small.png]] | ||
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[[Image:a_zalman_zm_m220w__2d_35_pic.jpg|150px|thumb|right|3d lcd]] | [[Image:a_zalman_zm_m220w__2d_35_pic.jpg|150px|thumb|right|3d lcd]] | ||
Control stereo separation / depth in coot 0.9: the transformation between the eyes is no longer a rotation and is now a shear. Which means that now we don't get part of the map showing up in the left eye but not the right (or vice versa). | |||
This is documented in Section 3.4.1, e.g. | |||
set_hardware_stereo_angle_factor(0.5) # for the Python fans | |||
Hardware stereo failure: try the line | |||
(set-display-lists-for-maps 0) | |||
in ~/.coot for coot 0.9 - see https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind2002&L=COOT&P=R312 and https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=COOT;49fa8d15.2006 | |||
==== Zalman Stereo ==== | ==== Zalman Stereo ==== | ||
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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. | 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=== | ===External Links=== | ||
====[ | ====[https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html On-line User Manual]==== | ||
====[ | ====[https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Coot's home page]==== | ||
====[http://www.mail-archive.com/coot@jiscmail.ac.uk/ Current mailing list archives]==== | ====[http://www.mail-archive.com/coot@jiscmail.ac.uk/ Current mailing list archives]==== | ||
==Scheme Scripts== | ==Scheme Scripts== | ||
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[[yellowify_molecule_keys.py]] | [[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== | ==Python to Scheme and return== | ||
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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: | 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 all '-' with '_' (except in equation when you need arithmetic '-' minus signs) | ||
# | # Move the brackets around the argument(s) | ||
# | # Separate multiple arguments by commas rather than spaces | ||
# | # Replace 'define' with 'def' for functions and with '=' for assignments | ||
# Make sure to use indentation for the function content [Python is indentation sensitive] and a ':' after the function definition. | # Make sure to use indentation for the function content [Python is indentation sensitive] and a ':' after the function definition. | ||
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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. | 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: The [https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#set_002dnomenclature_002derrors_002don_002dread Coot manual] should help: Add to your ~/.coot or whatever: | |||
(set-nomenclature-errors-on-read "ignore") | |||
In case you are using the python file, e.g. “.coot.py”, I think you have to change this to “set_nomenclature_errors_on_read ignore”. | |||
==NCS edits== | ==NCS edits== | ||
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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. | 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== | ==Image quality on NVidia cards== | ||
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A: there are 2 loop fitting tools in Coot | A: there are 2 loop fitting tools in Coot | ||
# C alpha -> Mainchain [http://lmb. | # C alpha -> Mainchain [http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#C_002dalpha-_002d_003e-Mainchain],[http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Building-Links-and-Loops] | ||
# DB Loop: (No good documentation) [http://lmb. | # DB Loop: (No good documentation) [http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#protein_002ddb_002dloops] Extensions -> Modelling -> DB Loop... | ||
==LSQ superpositions== | ==LSQ superpositions== | ||
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(let ((imol (read-pdb "test.pdb"))) | (let ((imol (read-pdb "test.pdb"))) | ||
(compare-ncs-rotamer imol "A" "B")) | (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. | |||
== specify Coot download directory, like specifying backup dir by COOT_BACKUP_DIR? == | |||
here is my working startup.py (of course replace src folder with your preferred location): | |||
import os | |||
try: | |||
os.symlink('/ccp4/xray/tmp/', 'coot-download') | |||
except: | |||
pass | |||
(Eugene Osipov on 22/04/2020 14:43) | |||