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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. | ||
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==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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===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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===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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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... | 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: | 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") | (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: 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. | 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) | |||