Notes on OLEX2 UBC Chemistry

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OLEX2 Manual,Table of Content,Table of Content 2,How to install OLEX2 under Windows 3. How to install OLEX2 on a Mac 6,Installing and using PLATON on a Mac 8. How to get OLEX2 to use PLATON 11,About program OLEX2 11. Keyboard shortcuts 12,Mouse traps 12,Alphabetical list of commands 13. Space group selection manipulation 42,Space group changes 45.
Additional structure manipulations 46, How to combine concatenate two or more commands into a macro command 48. Constraining the molecular geometry 50,When a solvent cannot be modeled 58. Working with molecular graphics 59,Structure matching 62. Working with hydrogen atoms 66,Making the structure look professional 67. Deriving metric data using GUI 68,General useful commands 69.
How to include instrument specifications in the CIF file 71. Comments on the Report feature 75,Working with Solid Angles 75. Some known issues 76,OLEX2 Manual,How to install OLEX2 under Windows. A The program is available as a free download from http www olexsys org just follow the. installation instructions from the web OLEX2 must installed and launched at least once in the. administrator mode in order for all features to work for all computer users You will also likely. need programs SHELXS and SHELXL written by George Sheldrick available free upon request. from http shelx uni ac gwdg de SHELX SHELXS and SHELXL are necessary for structural. solution and refinement respectively OLEX2 is smart and if you already SHELXS and SHELXL. or the entire SHELX suite installed OLEX2 is likely to find the programs on your computer If. it does not you ought to specify the path to the SHELXS and SHELXL files on your computer as. Suppose your SHELXL package is in folder C SAXI, Under Windows 7 open the properties panel Launch right click on Computer Properties. Under Advanced System Settings click on Environment Variables Under System Variables select. Path and add to the rather long line the following. Save and close Now Olex will list the supported programs in its structure solution and structure. refinement drop down menus, Q What other programs do I need and how do I install them. A OLEX2 can work seamlessly with other programs such as SHELXL PLATON XP superflip. and Pov ray The instructions below imply that you have licenses for the programs The. instructions are for Windows 7 and 8,0 Close OLEX2.
1 Download SHELXL from http shelx uni ac gwdg de SHELX and install it in. You may have to register it is free, 2 Put XP exe and superflip exe in the same folder C SAXI. 3 Download the PLATON for Windows Taskbar and PLATON executable and check def from. http www chem gla ac uk louis software platon and put them into. Make sure you put all PLATON related files into this folder. 4 Some environment variables need to be set as follows Go to Start Control Panel System. and Security System Advanced system settings, and in the System Properties window click on the Environment Variables button It may look. something like this,OLEX2 Manual, Under User variables for username click on New and in the Variable Name type. CHECKDEF and in the Variable value type c pwt check def as shown. OLEX2 Manual, If there is no PATH variable in the User variable for username section click on the New. button again and in the Variable name type,and for the Variable value type.
c saxi c pwt,as shown below, Click OK and close the windows you opened while navigating to the Advanced System Settings. 5 Start OLEX2 Let s check if the procedure worked Open a structure Go to Work Refine. and expand the Refinement Program dropdown menu If you installed the programs correctly you. should see at a minimum SHELXL and olex2 refine there. If you are not seeing SHELXL go back to the Advanced System Settings and modify the PATH. System variable rather than User variable to include c saxi To do so highlight the PATH. variable click Edit navigate to the end of this rather long line and append c saxi to the. end of the line Note the leading semicolon it is needed to separate the values on the line. Olex2 should be restarted for the changes to take effect If this does not work move the. c saxi part to the beginning of the Variable value line note the semicolon Olex2. should be restarted for the changes to take effect. OLEX2 Manual, Once SHELXL is visible select it in the dropdown menu put a checkbox next to the CONF. MORE 1 Bond h Acta line and run a refinement, Now click on the PLATON button located in the very top row. PLATON should launch and you should see PLATON s interface with all the buttons. If it does not work modify the PATH environment variable for the System similarly to the. suggestions for the c saxi above, Important if you launched PLATON successfully you need to close the PLATON interface and. PLATON generated windows before you can return to OLEX2 otherwise OLEX2 will hang and. PLATON will run in the background in which case it must be killed as a process in the Task. Optional Another good structure solution program Superflip can be downloaded from. http superflip fzu cz and it too should be placed in C SAXI folder. A computer restart may be necessary at this point,How to install OLEX2 on a Mac.
OLEX2 SHELX and XPREP Installation Instructions for Mac. by Brian Dolinar and from http www xrayforum co uk viewtopic php t 1838. In general it is helpful to refer to a list of commands for the OSX terminal such as the one found. here http ss64 com osx The terminal will be used throughout the installation process. Download and install OLEX2 from http www olexsys org You need OLEX2 version. 1 2 6 or later, 1 Register free as a new SHELX users at http shelx uni ac gwdg de SHELX. 2 Once you have registered a password will be emailed to you Navigate to the Downloads tab. Click the link provided at the bottom of the page that says download the programs When. prompted supply the username shelx and the password emailed to you. OLEX2 Manual, 3 You should now be looking at a file page that says Index of gsheldr bin Click the Mac. folder Then download the bz2 files you need For Ilia s class you will at least need shelxl. and shelxs, 4 Navigate to your Downloads folder and double click on the bz2 files you downloaded This. will extract your SHELX executable files to your Downloads folder. 5 Open the application folder for OLEX2 but do not run the program To open the folder right. click on the installed OLEX2 application icon in the Applications folder and select Show. package contents Then in the window that appears open the sub folders Contents and. 6 Place all the the SHELX executables you plan to use plus SHREDCIF in this folder. 7 Open an OSX Terminal window to make sure these files are executable. type cd Applications olex2 app Contents MacOS cd stands for change directory this. navigates to the place where you just put the SHELX executables. type chmod a x shelx shredcif, If this fails because of permissions repeat the instruction as. sudo chmod a x shelx shredcif,then give an administrator password.
this changes the permissions on all the SHELX programs and SHREDCIF to become. executable files and gives all users permission to run them. 8 Run the OLEX2 application Click the Work tab Then click the drop down arrow for the. Solve menu Verify that both olex2 solve and SHELXS listed as solution programs. 9 Click the drop down arrow for the Refine menu Verify that olex2 refine and SHELXL are. listed as refinement programs, 10 If you have a structure loaded you can verify that SHELXS and SHELXL work by running. them on that structure, XPREP This is for Chemical Crystallography at UW Madison only XPREP is not freeware. 1 Download XQuartz 2 7 7 dmg from http xquartz macosforge org landing This program. contains certain libraries that allow XPREP to work correctly Older computers may not need. this but newer ones do, 2 Open the dmg file then run the installer The installation will take 5 minutes Be patient. 3 To obtain XPREP download the program from the Box set up by Ilia Select the mac. 4 Once it is downloaded rename xprepformac to xprep. 5 In the terminal change the directory to your Downloads folder Do this by typing the. command cd and dragging the downloads folder into the terminal Press enter Your. terminal should now be in the Downloads folder, 6 Type the following command into your terminal chmod x xprep This changes the mode. on xprep to allow it to be executed by your computer The icon should also change from a. blank white icon to one that shows a black and green computer terminal. OLEX2 Manual, 7 Your terminal s directory should still be the folder that contains XPREP Run XPREP by.
typing xprep into your terminal If it works it will list some information about XPREP. and prompt you for a reflection file, 8 To run XPREP on a structure copy the executable into a folder with structurename hkl and. structurename p4p files in it Navigate the terminal to that folder Type in the terminal. xprep structurename, It should load the hkl and p4p files into xprep and show statistics about lattice centering. Installing and using PLATON on a Mac, By Anthony Linden Department of Chemistry University of Zurich Switzerland. anthony linden chem uzh ch, Here is how to get PLATON running on a Mac PLATON uses X11 for its GUI so you need the X11. libraries and tools and you then need a fortran compiler Ton Spek does not create compiled versions of. PLATON with static libraries hence you must compile it yourself and the need for all this. The instructions below should work on OS 10 13 High Sierra 10 12 Sierra and 10 11 El Capitan. The procedure sometimes changes a little for each new Mac OS version mainly because X11 libraries. sometimes change location and a PLATON executable compiled under one OS does not always work. under another Once you get this set up for one OS it works from then on at least until the next OS is. installed so you usually only need to do the actual compile step when updating PLATON It is advisable. to update and recompile PLATON at least once a month because it is constantly being improved. If you are familiar with Unix Linux the following is probably clear to you If not please simply try to follow. the instructions below exactly Please read and type carefully as there are important spaces and dashes. within some commands All commands typed in the XQuartz window are case sensitive Unix commands. usually do not give any feedback when they work correctly Messages often mean something might not. have worked, This looks long but is quite quick if all goes well Don t be discouraged.
The following is based on Ton Spek s readme at http www platonsoft nl xraysoft Mac OSX platon but I. have modified it a little to update the steps and remove the unnecessary installation of the full Xcode. developer kit Everything below is case sensitive Any other instructions or even a compiled version you. find on the PLATON web site might not be up to date. 1 Download the latest XQuartz 2 7 11 or later from http xquartz macosforge org. 2 Install it and start it located in Applications Utilities When the window opens you are in the top level. directory folder for your Mac user account To return here at any time type cd To find out which folder. you are in at any time type pwd, 3 Install Apple Command Line Tools Type in the XQuartz window xcode select install. 4 Download gcc and gfortran from http hpc sourceforge net. The binaries are near the top of the page be sure to choose the version appropriate for your Mac OS. version e g gcc 7 1 bin tar gz contains gcc and gfortran It is recommended you use Safari for the. OLEX2 Manual, download to avoid the tar files being completely unpacked after which the instructions below will not work. Firefox unfortunately unpacks the downloads, 5 Move these two files to your Desktop more convenient that way Probably your Mac automatically. uncompresses them so the gz is removed but you still must have the single files with the tar ending for. the next step, 6 In the XQuartz window type the following lines Note that uppercase spaces and dots are part of the. command and must be typed exactly as given add gz to the file names if they are still present with that. cd Desktop,sudo tar xvzf gcc 6 3 bin tar C, sudo asks for your login password the first time assuming you have administration rights Otherwise the.
password for the admin account on your Mac, 7 Create a folder named platon at a convenient location I use Desktop for now Note that if you use. uppercase letters for any part of the folder name then you must type it exactly the same way from now. 8 Download the files platon f gz xdrvr c gz check def sucrose spf from. http www platonsoft nl xraysoft unix platon and move them into that folder. 9 In XQuartz go to that folder If already at Desktop from the above then just type cd platon If lost. cd Desktop platon, 10 gunzip the files platon f gz and xdrvr c gz the Mac probably has done that automatically If not. gunzip platon f gz,gunzip xdrvr c gx, The file check def might have acquired the txt ending during the download If so type. mv check def txt check def, 11 Compile PLATON This is the most critical and often troublesome step Type carefully and exactly. sudo gfortran o platon platon f xdrvr c I opt X11 include L opt X11 lib lX11. Note that in the above the character after the dash in I opt is an uppercase i and the character after the. 2124 Chemistry Department University of Wisconsin Madison 1101 University Ave Madison WI 53706 USA This is work in progress You are encouraged to e mail me iguzei chem wisc edu

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