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RCrane, version 1.1 OVERVIEW RCrane allows for semi-automated building of RNA structure within Coot. This is done using the methodology described in: Keating KS and Pyle AM. Semiautomated model building for RNA crystallography using a directed rotameric approach. Proc Natl Acad Sci USA, 107: 8177-8182 (2010). and Keating KS and Pyle AM. RCrane: Semi-automated RNA model building. Acta Cryst D68: 958-995 (2012). Please note that all publications resulting from the use of RCrane must acknowledge the Acta Cryst manuscript. RCrane is copyright 2010-2012, Kevin Keating, and is licensed under the Educational Community License, Version 2.0. REQUIREMENTS RCrane requires Coot 0.6.2 or newer, and Coot must have been built with GTK2 and with Python scripting enabled. If you do not already have an appropriate version of Coot installed, it may be downloaded from http://lmb.bioch.ox.ac.uk/coot/software/binaries/releases/. If installing on Linux, you will need a build of Coot with "-python-gtk2" in the file name (i.e. coot-0.6.2-binary-Linux-i686-ubuntu-10.04.2-python- gtk2.tar.gz). If installing on Windows, use the WinCoot build (i.e. WinCoot-0.6.2.exe). Versions of Coot for OS X may be found at http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot. INSTALLATION RCrane is included with Coot 0.7 or newer. To launch RCrane, click on Extensions -> RCrane launch. If you are using Coot 0.6.2, you must install RCrane separately. To do this, first unzip rcrane.zip. If you are installing RCrane for all users of the computers, it is recommended that you put the RCrane directory within the Coot installation directory (e.g. /opt/coot/rcrane or C:\WinCoot\rcrane). If you are installing RCrane for only yourself, you may put the rcrane directory anywhere within your home directory (i.e. /home/name/Documents/rcrane or C:\Users\name\Documents\rcrane). TO RUN RCRANE FOR THE CURRENT COOT SESSION RCrane is included with Coot 0.7 or newer. To launch RCrane, click on Extensions -> RCrane launch. If you are using Coot 0.6.2, click on Calculate -> Run Script... Then choose launch.py within the RCrane directory. This will create an RCrane menu. TO AUTOMATICALLY LAUNCH RCRANE EVERY TIME COOT IS STARTED If you are using Coot 0.7, edit the rcrane.py file within your .coot- preferences directory. In Linux and OS X, this file is located at ~/.coot- preferences/rcrane.py. In Windows, this file is located within the WinCoot directory at WinCoot/.coot-preferences/rcrane.py. If the file does not exist, create it. Add the line rcane.createRCraneMenuWithCheck() to the file. If you are using Coot 0.6.2, click on Calculate -> Run Script... Then choose installRCrane.py within the RCrane directory. USING RCRANE - TRACING A NEW STRUCTURE To start a new RCrane trace, first move the center of the screen near where you would like to build the first phosphate, then select New Trace 5'->3'... from the RCrane menu. An RCrane window will appear and allow you to select the starting phosphate location. Once the desired phosphate is selected, click on the Accept button. RCrane will then attempt to trace the first nucleotide of the chain. If this is not the nucleotide you wished to build, then you may change the phosphate and base coordinates using the appropriate buttons. Once you are happy with the current nucleotide, click Accept Nt and RCrane will attempt to trace another nucleotide. After you have finished tracing a chain or chain fragment, accept the final nucleotide using the Accept Nt button and then click on Build Backbone. RCrane will then calculate the backbone atomic coordinates for the traced nucleotides. After coordinate calculation is complete, you will be able to review each suite and select alternate conformers where appropriate. USING RCRANE - ROTAMERIZING AN EXISTING STRUCTURE To rebuild a portion of an existing structure, select Rotamerize Existing Structure... from the RCrane menu, then click on atoms in the first and last suite you would like to rebuild. RCrane will calculate new backbone coordinates for the specified suites, and then allow you to review each suite and select alternate conformers where appropriate. Note that when you specify the region to rebuild, you are selecting suites and not nucleotides. Therefore, if you click on the phosphate of nucleotide 18, you have selected suite 18, which spans from the sugar of nucleotide 17 to the sugar of nucleotide 18. Also note that rotamerize will not work on portions of a molecule with insertion codes or alternate locations. Additionally, rotamerize currently clears all fixed atoms and custom restraints on the specified molecule when run. If you would like to rebuild an existing structure without taking electron density into account, select Rotamerize Without Density... instead. This is primarily intended for use when building theoretical models (i.e. when no electron density is available). Note that Rotamerize Without Density... is only available when running a version of Coot newer than r3728 (0.7-pre). USING RCRANE – EXTENDING AN EXISTING CHAIN To extend an existing chain, select Extend Chain… from the RCrane menu, then click on an atom in the nucleotide you wish to extend. RCrane will allow you to trace and build new nucleotides that extend the chain in either the 3' or 5' direction. If the new trace connects to an existing 5' or 3' terminus, clicking on Build Backbone will connect the new trace with the existing terminus. KEYBOARD SHORTCUTS Keyboard shortcuts can be assigned for starting a new trace or rotamerizing an existing structure. To set the keyboard shortcuts, see CUSTOMIZING RCRANE below. By default, no keyboard shortcuts are set. CUSTOMIZING RCRANE There are a small number of options that control how RCrane operates. Note that you do not need to set any of these options to use RCrane with the default settings. To change the options, first install RCrane (see TO AUTOMATICALLY LAUNCH RCRANE EVERY TIME COOT IS STARTED above). Next, edit the rcrane.py file within your .coot-preferences directory. In Linux and OS X, this file is located at ~/.coot-preferences/rcrane.py. In Windows, this file is located within the WinCoot directory at WinCoot/.coot-preferences/rcrane.py. If rcrane.py contains a run_python_script line, all setting commands must be added *after* that line. If you would like to add a keyboard shortcut for a new 5' to 3' trace, then add the line add_key_binding("New RCrane trace 5'->3'", "N", rcrane.newTrace5to3) and replace the "N " with the desired keyboard shortcut. Note that using an uppercase letter will create a shortcut for Shift+letter. If you would like to define a custom keyboard shortcut for a new 3' to 5' trace, then add the line add_key_binding("New RCrane trace 3'->5'", "M", rcrane.newTrace3to5) and replace the "M " with the desired keyboard shortcut. Note that using an uppercase letter will create a shortcut for Shift+letter. If you would like to create a keyboard shortcut for the rotamerization of existing structures, then add the line add_key_binding("RCrane rotamerize", "J", rcrane.newRotamerize) and replace the "J " with the desired keyboard shortcut. Note that using an uppercase letter will create a shortcut for Shift+letter. If you would like to create a keyboard shortcut for the rotamerization of existing structures without using the electron density, then add the line add_key_binding("RCrane rotamerize without density", "K", rcrane.newRotamerizeWithoutDensity) and replace the "K " with the desired keyboard shortcut. Note that using an uppercase letter will create a shortcut for Shift+letter. If you are using Coot 0.7 or newer and would like RCrane to automatically launch with Coot, add the line rcane.createRCraneMenuWithCheck() By default, RCrane limits the number of nucleotides that can be rotamerized at once (default: 20). This is done to prevent excessively long run times due to an erroneous mouse click. To increase the limit, add the line rcrane.setRotamerizeMaxNucleotides(40) and replace "40" with the desired limit. To remove the limit, add the line rcrane.setRotamerizeMaxNucleotides(-1) By default, RCrane uses REFMAC5 parameters for ideal bond lengths and angles during minimizations. These are the same parameters used by Coot during refinement or regularizement. To instead use the Phenix/MolProbity pucker- specific parameters in RCrane, add the line rcrane.enablePhenixRestraints() Note that this requires Coot 0.7-pre r3926 or later. To enable the Phenix/MolProbity restraints for the current session only, open Coot's Python scripting window (Calculate -> Scripting... -> Python...) and type the command rcrane.enablePhenixRestraints() To revert to the REFMAC5 parameters, type the command rcrane.disablePhenixRestraints() To determine the current parameter set, type the command rcrane.usingPhenixRestraints() A return value of True indicates that the Phenix parameters are being used. A return value of False indicates that the REFMAC5 parameters are being used. INSTALLING RCRANE FOR ALL USERS RCrane is included with Coot 0.7 and newer. If you are using Coot 0.6.2 on Linux and OS X, installing RCrane will only install it for the current user. Additional users must also follow the steps in TO AUTOMATICALLY LAUNCH RCRANE EVERY TIME COOT IS STARTED above. Alternatively, RCrane can be installed for all users of a computer by: 1. Install RCrane for the current user by following the instructions in TO AUTOMATICALLY LAUNCH RCRANE EVERY TIME COOT IS STARTED above. 2. Create a pyextras directory within the Coot installation directory (e.g. /opt/coot/pyextras). 3. Move ~/.coot-preferences/rcrane.py to the newly created pyextras directory. 4. Create the file /etc/profile.d/rcrane.sh containing the line: export COOT_PYTHON_EXTRAS_DIR=/opt/coot/pyextras (using the appropriate path for the pyextras directory). 5. Any users who are currently logged in must log out and log in again. RCrane will now be automatically launched with Coot for all users of the computer. UNINSTALLING RCRANE RCrane is included with Coot 0.7 and newer and cannot be uninstalled. If you are using Coot 0.6.2, you may prevent RCrane from running when Coot is started by deleting the rcrane.py file within your .coot-preferences directory. In Linux and OS X, this file is located at ~/.coot-preferences/rcrane.py. In Windows, this file is located within the WinCoot directory at WinCoot/.coot- preferences/rcrane.py. To completely uninstall RCrane from Coot 0.6.2, delete the RCrane directory as well.