On Febraury 9th, we processed a diffraction data set that Camila recently collected from APS, the synchrotron near Chicago. Efe logged the fix on the Teams channel for the course. Niña found a very useful fix for getting mosflm started, which involves fixing a typo in the startup script. Some people had trouble getting Mosflm to launch. The premise behind the fourier synthesis is that we know where the new structure is in the unit cell because we have seen it before. It works only if you have a known structure of the same (or mostly the same) biomolecule in the same space group as your new crystal. This is the easiest way to phase a structure. Determining a structure by fourier synthesis: The Phenix suite does many of the same things as the CCP4 suite (experimental phasing, molecular replacement, refinement, etc.) using different algorithms.Ģ.You must register as a user to get the password to download the software. Download and install the Phenix package (an alternative crystallographic processing package). RefMac from the CCP4 suite (see section A above) will calculate maps from structure factor files.Ĭ. Make sure you can open coordinates and maps in Coot.Or download your favorite coordinates from the PDB, save them as a text file, and open it from the file menu in Coot. Once you have installed Coot, open the program, from which you can download coordinates and structure factors from the Protein Data Bank ( PDB).If you are a Linux user, there are binaries available from the main Coot page here.If you are a Microsoft Windows user, there is a build for that OS here.I did an ugly workaround by going to the /usr/X11/lib directory and copying the updated library (which was libpng16.16.dylib after my X11 upgrade) to libpng12.0.dylib. Note for Mac Users: When I upgraded my X11 in March 2021, it broke Coot, where Coot couldn't find the file "/usr/X11/lib/libpng12.0.dylib".His site on Coot for OS X ( here) is tremendously useful for getting started. If you are a Mac user, there is a Mac OS X build on Bill Scott's website here.Download and install Coot (for building into electron density maps).Ĭoot is packaged with the CCP4 suite, or you can install a standalone version. Run the install tests in CCP4 to make sure your installation is working.ī.For example, "MacintoshHD/Users/Garman/Documents/Classes/Biochemistry/Spring2021/Biochem695a/February/FirstProject/DataProcessing/Trial1/" may not work with ccp4. It is probably best not to have more than a few folders above your working directory. Some people have had trouble when the working folder is really deep.The CCP4i graphic interface won't run correctly if you have spaces anywhere in your directory tree where you are running CCP4. Unix does not allow spaces in file and directory names. Beware of spaces in directories and file names.If you are installing on a laptop, make sure you have enough memory and storage space available.On a Mac, you need to have the X11 windowing software installed before you can install ccp4. Different operating systems will have different installations. Follow the instructions for installing the package.This package is a workhorse of X-ray crystallography software. Download the ccp4 suite of crystallographic programs. This year, we will determine a structure by fourier synthesis, determine a structure by molecular replacement, and combine diffraction data from different crystals.Ī. We will try to record the class for those who cannot attend in person. Please look at the Teams channel for the course, which has useful information and links we will use this semester. The Teams channel has a zoom code for the class. We meet at 3:00 on Wednesdays this semester in LGRT 745E. This year's journal club is organized by Scott Garman.
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