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(→make RSR in coot 0.8.1 behave like in earlier versions: Molprobity not active in COOT) |
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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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==== 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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[[morph_residues_gui.py]] | [[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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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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</pre> | </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. | 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. | |||