/***************************************************************************/ /* ENDEAVOUR - Structure Solution From Powder Diffraction Data */ /* Version 1.7g Update */ /*** ***/ /* (C) Copyright 2000-2015 Crystal Impact, H.Putz & K.Brandenburg GbR, */ /* Bonn, Germany. */ /* All rights reserved. */ /* Authors: Dr. Klaus Brandenburg, Dr. Holger Putz */ /*** ***/ /* Latest update of this Readme File: January 6, 2015 */ /***************************************************************************/ 0. Contents of this Readme File ------------------------------- 1. Installing Endeavour Update 2. What's new 3. Online Update 4. Online Support 5. Contacting Crystal Impact 1. Installing Endeavour Update ------------------------------ In order to update Endeavour to version 1.7g, you can either use the online update (see below), or perform the following steps: 1. If Endeavour is running, please close it. 2. Double-click on the file "Endeavour-Update-17g.exe" you have e.g. downloaded from the webpage. The installation program will start automatically and lead you through the update installation process. You can check whether the update was successful by selecting "About Endeavour..." from the "Help" menu. The Endeavour version displayed in the first line should be "1.7g". 2. What's new ------------- o Version 1.7g + If a CIF file contains both structure parameters and diffraction data, the user will now be prompted to open the CIF file either as structure or as diffraction file. + The "Auto Save" function is now enabled by default (cf. "Tools/Options"). + Several bugs have been fixed: ++ CIF files created by Shelx 2013 could cause trouble (hang-up or crash during file import), if they contained large data blocks with diffraction data, especially "_shelx_hkl_file" data blocks. ++ The CIF data item "_space_group_name_H-M_alt" (which supersedes "_symmetry_space_group_name_H-M") was not recognized (as Hermann-Mauguin symbol). So space group recognition could fail, if no additional symmetry operations were given or the attempt to recognize the space group from symmetry operations failed. ++ Some CIF files from ICSD were not read completely. (Import canceled after bibliographic data, thus no cell, space group and atomic parameter list were available. Example: Barium perchlorate (ICSD collection code 24272).) ++ Function "Tools/Potential Parameters": The fitted parameters A and C were not assigned, if the reference structure contains elements with the oxidation number "undefined" (rather than zero). ++ The advanced parameters "smooth_Fhkl_comparison" and "merge_reflections_Fhkl" of the "set" function were not recognized from and Endeavour script file (*.inp). ++ A bug in the kernel (Enkernel.exe) affecting charged molecules ++ A bug in the adjustment of potential parameters for molecular structures (Fit.exe) o Version 1.7f + Several bugs have been fixed: ++ Some improvements in space group recognition from Hermann-Mauguin, especially for symbols of rhombohedral space groups. ++ Export into CIF format corrected: Translational components in symmetry operations are now written as fractions, e.g. "x,y-1/2,z" instead of "x,y-0.5,z". (CIF/Platon syntax checker complainted that.) ++ When reading data from Shelx INS or RES file, FVAR variables were ignored. Thus a coordinate of "-22.000" was misinterpreted as -2.0 rather than "1.0 minus 2*FVAR(2)". ++ F-values and intensities were calculated too high, when the last three or more atoms in the atomic parameter list described the three or more components of one mixed site. (Components were taken into account redudantly leading to redundant addition of scatterings.) o Version 1.7e + Several bugs have been fixed: ++ Placed atoms' coordinates were unfixed during calculation, if value less than 0. (Now they are standardized to 0 <= {x,y,z} < 1.) ++ Sometimes loss of manually edited potential parameters when stepping back and forward through the Structure Solution Wizard. ++ Profile function "Intermediate Lorentzian" was not supported in the "Powder Pattern Settings" dialog and not displayed in the diffraction diagram view. ++ Some bugs (or potential misinterpretations) in the CIF import have been repaired. ++ "Origin choice 1" (non-centrosymmetric setting) was often set when importing structure data (e.g. from CIF), although "-x,-y,-z" was correctly given in the symmetry matrix loop. o Version 1.7d + Several bugs have been fixed: ++ User is now asked to restore documents resulting from a previous Endeavour or system crash. ++ No multiplicities or just "1" in the reflection parameter depending on option if to merge symmetry-equivalent reflections in imported data. ++ Symmetry-equivalent atoms in the parameter list are now marked and excluded from most building operations. ++ Cell parameters and space group may have been transferred incorrectly from the Diffraction Data Import Wizard. ++ Wrong multiplicities and too many reflections when calculating reflection data for some trigonal and hexagonal space groups. ++ No considering of hydrogen isotopes D and T for scattering coefficients and bond lengths. ++ Standard uncertainty of cell volume may be too big for angles different from 90 deg. ++ Selected atoms and bonds may be not correctly removed after "Build/Destroy/Fragments". o Version 1.7c + Additional page in Diffraction Data Import dialog: What to do with erroneous peaks as well as an option for zero-point correction. + The table of minimum interatomic distances for O-H, N-H, and F-H, used in automatic determination of structure solution parameters, has been updated. + Several bugs have been fixed: ++ Symmetry finding did not work on some MS Windows Vista implementations. ++ Diffraction Data Import dialog could hang up when checking file format. ++ Several bugs resolved dealing with invalid 2theta values of peaks, usually resulting from wrong given wavelength. ++ Error messages occurred and configuration was not created when calculating a structure without using diffraction data. o Version 1.7b + A bug has been fixed: ++ Some atomic form factors for electron diffraction were missing, e.g. for Ru. o Version 1.7a + The automatic check for available updates has been improved. Especially under Microsoft Windows Vista you will not be prompted unless an update is in fact available. + Several bugs have been fixed: ++ Command "Save Graphics" did not work to save diffraction diagram graphics in bitmap or Windows metafile format. ++ Command "Save Graphics" (for structure picture) did not store the latest used file format correctly. ++ When running command "Insert Diffraction Data" for an empty document, the page to enter the cell parameters was not shown in the "Diffraction Data Import" wizard, when you had chosen an hkl file format. o Version 1.7 + Optimizations for structure solution from electron diffraction data + Extended support for single crystal diffraction data (|F(hkl)|, F^2(hkl) and I(hkl)) ++ Merging of symmetry-correlated or Friedel reflections imported from hkl data files ++ Option for influence reduction of I(hkl) (or |F(hkl)|) differences if I(hkl) > 0 + New tutorial chapter demonstrating structure solution from electron and other single crystal diffraction data + Several bugs have been fixed o Version 1.6x + Automatic adjustment of all structure solution calculation parameters + Calculated profile function can be used instead of peaks for R-factor calculation, in order to avoid peak assignment problems + Automatic determination of space group from structural model (no need to adjust tolerance parameters anymore!) + Settings for the structure visualization "Autobuild" function (e.g. molecules, polyhedra) can now be adjusted automatically, taking into account the "chemistry" of the compound under investigation + Minimum interatomic distances for all element pair combinations (derived from "Pearson's Crystal Data") are now implemented (no need for manual adjustment of parameters for the simple repulsion potential anymore) + New separate pane for configuration list in Endeavour window + Chapter "Tips&Tricks" in the manual now contains a lot more hints on what you could do if your structure is not directly solved by Endeavour + Bugs that have been resolved in version 1.6: ++ Demoversion reported error "licence expired" without any reason, so Endeavour did not run in full featured mode for two months ++ Kernel crashed if more than 50 atoms were present in the parameter list ++ Fixed atoms did not hold their position or were even deleted ++ If the Endeavour document file name contained blanks, the kernel did not start the calculation. o Version 1.5x + Bugs that have been resolved in version 1.5a: ++ If a CIF file contained only a "data_global" block AND blank lines preceded the "data_global" line, Endeavour reported an error message "No structure data found...". ++ When you ran a structure solution in a space-group other than P1, then changed the space group and ran again, you might receive an error message "Error position nnnx not found in space-group Y..." where nnn and x are multiplicity and Wyckoff letter of the position in the space group with Hermann-Mauguin symbol Y. ++ When you chose a space-group setting on page 1 of the structure solution wizard where no Wyckoff position information was available, the structure solution stopped with an error message "Error position...not found in space-group... Probably unknown setting." ++ When you set the "Cost function balance" (page 6 of structure solution wizard) to 0 (leftmost position, i.e. potential energy was considered only but not the differences in diffraction data), the structure picture etc. was not updated during calculation and when calculation was finished. "Undo" was not available for that solution step, too. ++ The Angstroem symbol was not correctly readable on Japanese Windows versions, e.g. in "Powder Pattern Settings" dialog (Diffraction menu). + Advanced settings that affect handling of molecules, single atoms as well as the treatment of peaks, calculation of R-value, and the optimization can now be changed by the user allowing much more influence and experiments to the optimization results. (Available from structure solution wizard.) + Optional zero-point correction after import of peak data. + Automatic checking of peak correlations. + New desktop design like in Diamond v.3 (menus, toolbars, configuration list, data sheet). + Separate command to open a molecule structure file avoiding misleading when solving a crystal structure containing molecules. ("File/New Structure Solution" and "File/ New Molecule...".) + Kernel Scripting Reference and Structure Data File Formats Reference available from the Help menu. o Version 1.4x + Bugs that have been resolved in version 1.4a: ++ Dummy atom scattering factors were not written into Endeavour kernel script file when single dummy atoms were placed or at least one rigid body molecule contained at least one dummy atom. (It already worked for non-placed single atoms.) ++ Lennard-Jones potential parameter fit could not properly consider atoms from a CIF reference structure file when no oxidation numbers were given. The number of reference structures is not more limited to 5. ++ The settings for "placed" molecules: "fixing" and "allow rotation" got lost after an optimization run of the Endeavour kernel. ++ Endeavour "forgot" about the fixing of atoms if more than 50 atoms were present in the asymmetric unit. ++ The "Assign peaks" dialog (called from page 4 of "Structure Solution Wizard") did not list and draw calculated peak positions, if total 2theta range in "Powder pattern settings" dialog (can also be called from page 4 of wizard) was set to "auto". ++ Several bugs led to problems if an interrupted calculation was continued ("restarted"). + Molecules can now be rotated around a reference atom which has been fixed to a certain position. + The structure solution wizard has been significantly improved concerning the handling of molecules. For example, you can place and fix molecules at certain positions by clicking on the "Place molecule(s)..." button on page 2 of the structure solution wizard. + Checking of unit cell parameters: Before the actual structure solution calculation is started, Endeavour now compares the peak positions calculated from the unit cell parameters to the experimental values and displays a warning if a large deviation is found. + Some internal optimization parameters have been optimized. + Hofmann potential: This potential which has been derived from distance statistics by Dr. D. Hofmann is extremely powerful in the solution or even prediction of crystal structures of rigid organic molecules (D.W.M. Hofmann, J. Apostolakis, "Crystal structure prediction by data mining", J. Mol. Struc. (Theochem) 647, 17-39 (2003)). Another advantage of this potential is that there are no parameters which have to be adjusted by the user, so that its usage is extremely simple. + Online update: You can now update Endeavour online directly from within the program. By default, Endeavour will check the Crystal Impact webserver automatically for new versions each time Endeavour is executed. If a more recent version has been found, it is downloaded and installed automatically. For more information, read the chapter "Online Update" below. + Bugs that have been resolved in version 1.4: ++ Four severe bugs (typing errors) in the parameter table for the atomic form factor calculation for X-ray radiation have been resolved. The following elements were affected: H, Sc3+, Ru4+, Bi5+ The wrong parameters caused deviations in the calculated intensities, probably even preventing some crystal structures from being solved. ++ A bug leading to the distorted display of atoms and other objects on wide screen displays with a width/height ratio different from 4:3 has been resolved. ++ When you exported a structure into CIF format and at least one atom symbol was blank (cf. command "Structure/Atomic parameters..."), the CIF caused trouble when reading into Endeavour again. ++ Some minor bugs have been fixed. o Version 1.3x + Bugs that have been resolved in version 1.3b: ++ In some cases, if atoms were placed, the "Define atoms in unit cell" page (Page 3 of 7 of "Preparation of structure solution" wizard) showed negative counts in the list. ++ In some cases, if all atoms were placed but contained at least some unfixed parameters, the option "Local refinement" was yet possible. + Bugs that have been resolved in version 1.3a: ++ If a second or third etc. molecule was referenced in an Endeavour Script input file, the atoms of the second molecule were appended to the atoms of the first read molecule. In some cases Endeavour crashed due to subsequent reading errors. ++ In some cases, the symbols of the atoms in the parameter list were not updated after "Preparation of structure solution" wizard. ++ When ending the "Preparation of structure solution" wizard with "Create input files only but do not run kernel", the Endeavour document was not marked as modified and the views (structure picture, data sheet, etc.) were not updated. 3. Online Update ---------------- Endeavour is able to automatically download and install a new version once it has become available. It connects to the Crystal Impact webserver and compares the version of the most recent update available there to the version which is currently installed on your PC. In order to achieve this, a working connection to the internet is required, of course. If you are not connected to the internet, Endeavour will ask you to do so before continuing. If a more recent version is found on the webserver, a list of changes and improved features in the new version will be displayed, and you will be asked if you would like to download the corresponding update. Once you have acknowledged and the corresponding files have been downloaded, you will be asked to close all open Endeavour windows so that the update program can replace the program executable. After the update has been completed, Endeavour will be restarted so that you can check if the update was successful. This can e.g. be achieved by selecting the "About Endeavour..." command in the "Help" menu and checking the version number and date in the dialog which is displayed. By default, Endeavour checks the Crystal Impact webserver for a new version automatically each time it is executed. If you would like to disable this feature (e.g. if you are not permanently connected to the internet), you can do so on the "Desktop" page of the "Tools/Options" dialog, simply by removing the hook in front of "Check for available updates when starting" at the bottom of the dialog. Even if you have disabled the "Automatic update checking" option, you can update your software online by selecting the "Online update" command from the "Help" menu. The procedure will be the same as the one described above for the automatic update. 4. Online Support ----------------- In case of trouble with Endeavour, please refer to the Endeavour Support Page on the Web, which has the address: http://www.crystalimpact.com/endeavour/support.htm Or send an e-mail to: support@crystalimpact.com 5. Contacting Crystal Impact ----------------------------- To contact a Crystal Impact representative, either... - send e-mail to: info@crystalimpact.com - fax to: +49-228-9813644 - call: +49-228-9813643 - or write to: Crystal Impact, Kreuzherrenstr. 102, D-53227 Bonn, Germany. You can also visit the Endeavour webpage at http://www.crystalimpact.com/endeavour/index.html