Welcome to my website!
Miscellaneous information and resources
Here I enlist different resources that I utilize for my work and analysis. They are not supposed to be in any particular order, I add them here as and when I come cross them or remember them. Hope some of it is useful to as well.
Cryo-EM packages : SPA and Cryo-ET
1. Relion 4.0
https://github.com/3dem/relion
follow the procedures described in: https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Download%26_install
> source ~/relion.login
> git clone https://github.com/3dem/relion.git
> cd relion
> git checkout ver4.0
> git pull > mkdir build-gcc; cd build-gcc
> cmake -DCUDA_ARCH=75 -DCMAKE_INSTALL_PREFIX=/usr/local/relion ..
> make -j 8 >& make.log
> sudo make install
2. Dynamo - a software environment for subtomogram averaging of cryo-EM data.
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https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Main_Page
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I have tested the versions 4.11.1.532 and 4.31.1.514​. Dynamo can be somewhat buggy during runs and may need time to test various parameters. The installation also needs an Matlab installation or just Math libraries which are shipped with a Dynamo installation, in case you do not have a Matlab licence.
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> cd <DYNAMO_ROOT>
> tar -xf dynamo-v-1.1.157_MCR-9.0.0_GLNXA64.tar
> tar -xf <absolute path to tar file> -C <DYNAMO_ROOT>
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Run matlab and then run Dynamo.
3. MOTIONCOR2.
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Download it from https://emcore.ucsf.edu/ucsf-software. Get the latest version that supports the CUDA version you have installed.
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> sudo cp Motion2_1.5.0-Cuda116_05-31-2022 /usr/local/bin/.
4. CTFFIND4.
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Download CTFFIND 4.1.14 from https://grigoriefflab.umassmed.edu/ctf_estimation_ctffind_ctftilt.
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> sudo apt install libwxgtk3.0-dev
> tar vxfz ctffind-4.1.14.tar.gz
> cd ctffind-4.1.14
> ./configure
> make
> sudo make install
5. ResMap.
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Download it from: http://resmap.sourceforge.net/.
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> chmod 755 ResMap-1.1.4-linux64
> sudo mv ResMap-1.1.4-linux64 /usr/local/bin/.
6. ChimeraX.
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Download it from: https://www.cgl.ucsf.edu/chimerax/
Easy GUI based installation. Further resources are here https://www.cgl.ucsf.edu/chimerax/docs/index.html
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7. Phenix 1.20.1.
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Download it from: https://www.phenix-online.org/.
> tar vxfz phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6.tar.gz
> cd phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6
> sudo ./install
8. Phenix 1.20.1.
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Download it from: https://github.com/timothygrant80/cisTEM.
> git clone https://github.com/timothygrant80/cistem.git
> cd cisTEM
> mkdir build
> cd build
> ../configure
> make
> make install
9. Eman2.
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Download it from: https://blake.bcm.edu/emanwiki/EMAN2. Last, I tested the version v2.91. Eman2 is an excellent package with abilities for both SPA, STA and segmentation.
Follow the instructions here https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda/2.91
9. CryoSPARC.
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Download it from: https://cryosparc.com/. You will have to register to get an installation link.
10. CrYOLO.
Detailed installation instructions with the conda environment and installing napari plugin are present on the following page.
Download it from: https://cryolo.readthedocs.io/en/stable/installation.html
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10. Homolmapper - to plot conservation on PDB b-factors for visualization.
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Download it after seeing the licence agreement: https://lagariaslab.faculty.ucdavis.edu/homolmapper/
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11. IsoNet : Isotropic Reconstruction of Electron Tomograms with Deep Learning
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Download and extensive installation instructions for version 0.2 : https://github.com/IsoNet-cryoET/IsoNet
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12. IMOD
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Download and extensive installation instructions here : https://bio3d.colorado.edu/imod/
13. TomoBEAR
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Download and extensive installation instructions here : https://github.com/KudryashevLab/TomoBEAR
15. SCIPION
Installation instructions here : https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html
Experimental design and analysis
1. Fiji - Fiji is ImageJ, The creators did have a sense of humour while choosing this name.
Anyone working with image analysis would have used this software. Versatile and open access.
https://imagej.net/software/fiji/
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2. Useful website for people working with ultracentrifugation.
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One can do a variety of rotor calculation here https://www.sciencegateway.org/tools/rotor.htm
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In case you don't find a rotor here, chances are it a relatively new rotor and does not fall in the classical ultra rotors. The website if still fun to also compare rotors between manufacturers. A not so famous hobby I must admit :-p
3. OpenWetWare : One of my favourite e-lab notebook tools.
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I owe a great deal to the open methods available here, esp. during my PhD, when I used was learning ribosome biochemistry from classical ribosome literature and lab notebooks of unknown researchers at OpenWetWare.
https://openwetware.org/wiki/Main_Page
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4. ApE : A plasmid editor
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A simple, effective and no nonsense tool for editing and designing plasmids. Though it has an issue of not being able to have internal libraries and storing large datasets, as a standalone tool its fantastic.
Download jere https://jorgensen.biology.utah.edu/wayned/ape/.
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5. Benchling - A cloud based alternative to benchling, snapgene etc.
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Useful for editing, and designing Oligos. Register and use it here https://www.benchling.com/.
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7. Inkscape.
Open source alternate to illustrator and paid packages.
Download it from: https://inkscape.org/.
8. Affinity Designer.
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This is a paid graphic design software and is an excellent alternate to Adobe Illustrator. In addition, it is a one time purchase rather than most annual permits from Adobe. Download it from: https://affinity.serif.com/en-gb/.