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| 3 | <title>EXPGUI</title> |
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| 4 | <meta name="keywords" content="crystallography, Rietveld, diffraction, |
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| 5 | GSAS, EXPGUI"> |
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| 11 | |
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| 12 | <BODY BGCOLOR="#FFFFFF" |
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| 14 | text="#000000" link="#0033ff" vlink="#0033ff" alink="#0033ff"> |
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| 16 | <? |
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| 17 | include("/var/www/include/navigation.inc"); |
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| 18 | include("/var/www/include/utility.inc"); |
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| 19 | ?> |
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| 20 | <blockquote><font face="arial, helvetica, sans-serif"> |
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| 21 | |
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| 22 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
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| 23 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
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| 24 | </TH><TH><A Href="liveplot.html">Next page<BR>(Utilities)</A> |
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| 25 | </TH><TH><A Href="expgui7.html">Previous page</A> |
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| 26 | </TH></TR></TABLE><BR CLEAR=ALL> |
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| 27 | |
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| 28 | <center><h1> |
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| 29 | <HR noshade width="75%" size="2" align="center"> |
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| 30 | EXPGUI, Menu Contents |
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| 31 | <HR noshade width="75%" size="2" align="center"> |
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| 32 | </h1></center> |
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| 33 | |
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| 34 | <h2>C. Menu Contents</h2> |
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| 35 | Note that the figures on this page are likely to be out of date with |
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| 36 | respect to the text. The text is updated more frequently. Also, note |
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| 37 | that not all menu options are available in Windows. |
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| 38 | |
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| 39 | <a name="1"></a> |
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| 40 | <H3>C.1 File Menu</H3> |
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| 41 | <BLOCKQUOTE> |
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| 42 | The options on the File menu as is the custom contains the commands |
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| 43 | for reading and writing experiment files, as well as starting |
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| 44 | and ending the program. |
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| 45 | <DL> |
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| 46 | <DT>Open<DD> |
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| 47 | Select an existing GSAS experiment to be used. If a name is entered |
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| 48 | that does not exists, it is possible to create a new |
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| 49 | experiment file from scratch. |
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| 50 | <DT>expnam<DD> |
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| 51 | Equivalent to Open (included for historical reasons.) |
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| 52 | |
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| 53 | <DT>Save<DD>Saves modifications to the current experiment file to disk (shortcut Alt-S). |
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| 54 | <DT>Save As<DD>Saves modifications to the current experiment file to disk |
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| 55 | under a new file name |
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| 56 | <DT>Reread .EXP file<DD>Reread the last saved version of the |
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| 57 | experiment file from disk. |
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| 58 | <DT>Update GSAS/EXPGUI<DD>This queries the EXPGUI software repository |
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| 59 | to see if any files in EXPGUI or GSAS has been updated. It then |
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| 60 | offers the program user the option to update these files. The update |
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| 61 | will fail if the user does not have permission to change the EXPGUI |
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| 62 | or GSAS files. In this case, a system administrator may be needed. |
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| 63 | <DT>revert<DD>Used to load an <a href="#archive">archived</A> |
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| 64 | (backup) version of the current .EXP file. |
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| 65 | <DT>EraseHistory<DD>Deletes old history records to speed reading of the .EXP file. |
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| 66 | <DT>convert<DD>Convert a standard ASCII file to the direct access |
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| 67 | format used by GSAS (and for UNIX, the reverse) -- this is not |
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| 68 | likely to be needed, as GSAS now does most conversions automatically. |
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| 69 | <DT>exit<DD>Exit EXPGUI (shortcut Alt-X or ^C) |
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| 70 | </DL> |
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| 71 | <img SRC="m1.gif" BORDER=3 alt="EXPGUI Screen snapshot"> |
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| 72 | </BLOCKQUOTE> |
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| 73 | |
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| 74 | <a name="2"></a> |
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| 75 | <h3>C.2 Options Menu</h3> |
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| 76 | <BLOCKQUOTE> |
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| 77 | This menu contains options that determine how EXPGUI runs. |
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| 78 | <a name="archive"></a> |
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| 79 | <DL> |
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| 80 | <DT>archive EXP<DD> |
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| 81 | Toggles archiving of .EXP files. When on, files are |
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| 82 | saved before they are overwritten by EXPGUI as a file |
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| 83 | named <I>EXPNAM</I>.Oxx where xx is a pair of hexidecimal |
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| 84 | digits (01, 02,..., 09, 0A,... OF, 10,... FF). |
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| 85 | Each time that EXPGUI archives a file, note is placed in the .LST file |
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| 86 | so that the saved file name can be associated with |
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| 87 | the refinement stage. Turning this option off, prevents EXPGUI |
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| 88 | from creating these <I>EXPNAM</I>.Oxx archive files, but |
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| 89 | the will still be created by EXPEDT, GENLES,... |
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| 90 | <P> |
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| 91 | <DT>Use DISAGL Window<DD>When this option is set, results from DISAGL are |
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| 92 | shown in a separate window. When it is not set, the results are |
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| 93 | written in the .LST file. Note that on Windows, LSTVIEW can interfere |
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| 94 | with putting output into the DISAGL window. The solution is to |
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| 95 | close LSTVIEW before running DISAGL. |
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| 96 | |
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| 97 | <a name="Autoupdate"></a> |
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| 98 | <DT>Autoload EXP<DD>Normally EXPGUI prompts before rereading the EXP |
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| 99 | file when GENLES, POWPREF,... or other GSAS programs run |
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| 100 | If this option is set, the new file is automatically read without a prompt. |
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| 101 | The advantage of leaving this option off, is that |
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| 102 | you can opt to not load the |
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| 103 | revised .EXP file, which means that you reject the last set of changes. |
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| 104 | This is useful if |
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| 105 | GENLES blows up or you have done something wrong. The reason to |
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| 106 | turning "autoload EXP" on is |
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| 107 | that there is one less thing to do when running GSAS programs. |
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| 108 | Note that it is still possible to reverse changes, if |
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| 109 | <a href="#archive">archive files</A>, but this may require more |
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| 110 | effort. See the File/revert menu entry. |
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| 111 | <a name="execprompt"></a> |
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| 112 | <DT>Prompt after GSAS run<DD> |
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| 113 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
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| 114 | By default, GSAS programs are run in a separate window |
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| 115 | and after the program completes, the window remains open until enter is |
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| 116 | pressed in the window. Turning the "Prompt after GSAS run" option off, causes |
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| 117 | the window to be closed immediately after the program completes, saving |
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| 118 | some effort but obliterating any error messages or other evidence of problems. |
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| 119 | |
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| 120 | <a name="Autoicon"></a> |
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| 121 | <DT>Iconify during GSAS<DD> |
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| 122 | If this option is turned on, the main EXPGUI window is shrunk to an icon |
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| 123 | (minimized) while GSAS programs are running and EXPGUI is suspended. |
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| 124 | The author prefers this mode, since there is no reason to have the |
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| 125 | screen cluttered with EXPGUI when it can't be used, |
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| 126 | but this is an option so that the mode can be turned off by those people |
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| 127 | who find this behavior annoying. It appears this option causes |
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| 128 | problems on Windows 7. |
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| 129 | |
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| 130 | <a name="AutostartGRWND"></a> |
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| 131 | <DT>Autostart GRWND |
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| 132 | <DD> |
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| 133 | This option is available on Windows-95, -98 and -ME to deal with a operating |
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| 134 | system quirk that prevents the starting of the GRWND.EXE program, |
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| 135 | needed for graphics in GSAS programs such as POWPLOT, RAWPLOT, EXPEDT,... |
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| 136 | (this program is not needed for EXPGUI graphics, such as LIVEPLOT). It |
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| 137 | is not understood why this error happens or how to prevent it. One cure |
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| 138 | is to start this GRWND.EXE program before starting the GSAS program. |
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| 139 | If this option is selected, each time a GSAS program is started, a separate |
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| 140 | program TLIST.EXE is used to check if GRWND.EXE is running. If it is not, |
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| 141 | EXPGUI will start this program before starting the requested GSAS program. |
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| 142 | |
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| 143 | <a name="sortatoms"></a> |
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| 144 | <DT>Sort atoms by<DD> Determines the order that atoms are displayed on the "Phase" pane |
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| 145 | Atoms may be displayed sorted by number, atom type, site multiplity, |
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| 146 | occupancy, or by x, y or z coordinate |
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| 147 | <P> |
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| 148 | Clicking on the heading above the atoms list cycles with the left |
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| 149 | mouse button cycles through the atom sort modes. Clicking with |
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| 150 | the right mouse button resets the atom sort mode to "number". |
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| 151 | |
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| 152 | <a name="sorthist"></a> |
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| 153 | <DT>Sort histograms by<DD>Determines the order that histograms are displayed on the |
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| 154 | Histogram, Scaling and Profile panes |
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| 155 | |
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| 156 | Histograms may be sorted by histogram number, histogram type, |
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| 157 | original bank number, or diffraction angle/wavelength |
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| 158 | <DT><A href="expgui.html#multiplehistogram">Multiple hist. selection</A><DD> |
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| 159 | When this mode is off, it is possible to modify parameters |
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| 160 | and refinement flags for only a single histogram. For other settings, |
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| 161 | it is possible to modify parameters and flags for groups of |
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| 162 | histograms (see help for Mouse actions). |
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| 163 | |
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| 164 | It does not make sense, however, to globally modify |
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| 165 | instrument-related parameters and flags for different histogram types. |
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| 166 | So global actions can be limited to a single class of histogram types |
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| 167 | (e.g. TOF, CW Neutron,...), which allows these parameters to be set |
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| 168 | for groups of similar histograms. Thus, if this mode is set to "All" |
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| 169 | the Histogram and Profile panes are disabled. |
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| 170 | <DT>Override backspace<DD>This option is available in UNIX only, as there are different |
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| 171 | ways that backspace can be implemented. When option is set |
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| 172 | as "On," the backspace key is overridden to send a "delete" |
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| 173 | character. If backspace does not work in a program such as |
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| 174 | EXPEDT, change try the other setting for this option. |
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| 175 | |
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| 176 | <a name="setfont"></a> |
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| 177 | <DT>Set Screen Font |
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| 178 | <DD> |
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| 179 | This menu changes the fonts used in most sections of EXPGUI. |
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| 180 | Note that this setting can be saved with the |
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| 181 | SaveOptions menu option (below) so that EXPGUI automatically |
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| 182 | starts with the chosen font. |
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| 183 | |
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| 184 | <a name="exptoolout"></a> |
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| 185 | <DT>Show EXPTOOL output<DD> |
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| 186 | Normally EXPGUI does not show the output from EXPTOOL, when |
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| 187 | actions like adding atoms, phases or histograms is performed. |
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| 188 | If an error is detected, the output is shown. If |
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| 189 | there are problems with adding phases, atoms, histograms... and |
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| 190 | a window showing an error does not appear, |
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| 191 | this option should be set to "on" so the output from EXPTOOL is |
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| 192 | always shown. |
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| 193 | |
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| 194 | <DT>Save Options<DD>Save the current values for "Override backspace", |
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| 195 | <a href="#sortatoms">"Sort atoms by"</a>, |
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| 196 | <a href="#sorthist">"Sort histograms by"</a>, |
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| 197 | <a href="#archive">"archive EXP"</a>, |
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| 198 | <a href="#Autoupdate">"Autoload EXP"</a>, |
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| 199 | <a href="#setfont">"Set Screen Font"</a>, |
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| 200 | and |
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| 201 | <a href="#Autoicon">"Iconify during GSAS"</a> |
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| 202 | |
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| 203 | in file ~/.gsas_config (or c:\gsas.config on Windows). |
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| 204 | <DT>Save Position<DD>Saves the current screen position of the EXPGUI |
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| 205 | window as the starting point for future runs of EXPGUI in |
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| 206 | in file ~/.gsas_config (or c:\gsas.config on Windows). |
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| 207 | |
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| 208 | <DT>liveplot_options<DD>Used to set options for |
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| 209 | <a HREF="liveplot.html#liveplot">LIVEPLOT</a>, |
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| 210 | for example, the histogram to be plotted |
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| 211 | <DT>Assign app to .EXP files<DD>(on Mac only) When selected, this |
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| 212 | causes .EXP files to be linked (via the file resource fork) to the |
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| 213 | EXPGUI applescript. This also causes the .EXP files to be displayed |
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| 214 | with a GSAS icon. |
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| 215 | |
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| 216 | </DL> |
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| 217 | <img SRC="m2.gif" BORDER=3 alt="EXPGUI Screen snapshot"> |
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| 218 | </BLOCKQUOTE> |
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| 219 | |
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| 220 | <a name="3"></a> |
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| 221 | <h3>C.3 Powder Menu</h3> |
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| 222 | <BLOCKQUOTE> |
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| 223 | This menu contains links to GSAS programs used for powder diffraction |
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| 224 | analysis. |
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| 225 | <DL> |
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| 226 | <DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E) |
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| 227 | <DT>powpref<DD>Powder data preparation (shortcut Alt-P) |
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| 228 | <DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G) |
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| 229 | <DT>powplot<DD>Display powder patterns |
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| 230 | <DT>rawplot<DD>Plot powder data |
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| 231 | <DT>fitspec<DD>Fit a TOF vanadium scattering spectrum |
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| 232 | <DT><a HREF="liveplot.html#bkgedit">bkgedit</a> |
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| 233 | <DD>Invokes the <a HREF="liveplot.html#bkgedit">BKGEDIT</a> program |
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| 234 | to fit a background function to a set of fixed background points. |
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| 235 | <DT><a HREF="excledt.html">excledt</a> |
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| 236 | <DD>Invokes the <a HREF="excledt.html">EXCLEDT</a> program |
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| 237 | to set the upper and lower limits for a histogram, as well as |
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| 238 | edit excluded regions. |
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| 239 | <DT>seqgsas<DD>Invokes the sequential GSAS refinement program to run |
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| 240 | GENLES on a set of very similar data files. |
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| 241 | <DT>mustrplot<DD>Plot microstrain results |
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| 242 | <DT><a HREF="expgui.html#INSTEDIT">instedit</A><DD>Invokes the <a HREF="expgui.html#INSTEDIT">instedit</A> |
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| 243 | to edit an instrument parameter file. |
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| 244 | <DT>New InstParm file<DD>Creates a new instrument parameter file using |
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| 245 | <a HREF="expgui.html#INSTEDIT">instedit</A>. |
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| 246 | |
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| 247 | |
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| 248 | </DL> |
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| 249 | <img SRC="m3.gif" BORDER=3 alt="EXPGUI Screen snapshot"> |
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| 250 | </BLOCKQUOTE> |
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| 251 | |
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| 252 | <a name="4"></a> |
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| 253 | <h3>C.4 Xtal (Single Crystal) Menu</h3> |
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| 254 | <BLOCKQUOTE> |
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| 255 | This menu contains links to GSAS programs used for |
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| 256 | single-rystal diffraction analysis. |
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| 257 | <DL> |
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| 258 | <DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E) |
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| 259 | <DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G) |
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| 260 | <DT>scabs<DD>Single crystal absorption |
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| 261 | <DT>scmerge<DD>Sort and merge single crystal data |
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| 262 | <DT>sxtldata<DD>Prepare generic single crystal data |
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| 263 | </DL> |
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| 264 | <img SRC="m4.gif" BORDER=3 alt="EXPGUI Screen snapshot"> |
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| 265 | </BLOCKQUOTE> |
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| 266 | |
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| 267 | <a name="5"></a> |
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| 268 | <h3>C.5 Graphics Menu</h3> |
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| 269 | <BLOCKQUOTE> |
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| 270 | This menu contains links to several GSAS and |
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| 271 | two non-GSAS (<a HREF="liveplot.html#liveplot">LIVEPLOT</a>, |
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| 272 | and widplt) |
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| 273 | programs used for graphical display of data and results. |
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| 274 | <DL> |
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| 275 | <DT>Fourier<DD>Provides an interface to set up computation of |
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| 276 | Fourier maps and compute them using program Fourier. |
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| 277 | Also see the <A HREF="#DRAWxtl">Export to DRAWxtl</A> interface, |
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| 278 | which can be used to set up, compute, export and display Fourier |
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| 279 | maps. Note that a Fourier map can be set up for only one phase |
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| 280 | at a time. |
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| 281 | <DT>forsrh<DD>Search Fourier map for peaks |
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| 282 | <DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT |
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| 283 | and then compute with FOURIER |
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| 284 | <DT>polfplot<DD>Display polefigures |
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| 285 | <DT>powplot<DD>Display powder patterns |
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| 286 | <DT>ortep<DD>Draw crystal structure |
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| 287 | <DT>rawplot<DD>Plot powder data |
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| 288 | <DT>gsas2map<DD>Exports a Fourier map in formats used by other |
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| 289 | programs (for example Fox and DRAWxtl). |
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| 290 | <DT><a HREF="liveplot.html#liveplot">liveplot</a> |
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| 291 | <DD>Invokes the <a HREF="liveplot.html#liveplot">LIVEPLOT</a> program |
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| 292 | to create a plot of powder data |
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| 293 | with zooming, automatic update and other nice features. |
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| 294 | <DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software |
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| 295 | <DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file |
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| 296 | <DT><a HREF="expgui.html#ABSPLT">absplt</A> |
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| 297 | <DD>The <a HREF="expgui.html#ABSPLT">absplt</A> program displays the |
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| 298 | absorption/reflectivity correction curve for values used in a histogram. |
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| 299 | <DT>mustrplot<DD>Plot microstrain results |
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| 300 | <DT>seqplot<DD>Plot results from seqgsas |
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| 301 | </DL> |
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| 302 | <img SRC="m5.gif" BORDER=3 alt="EXPGUI Screen snapshot"> |
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| 303 | </BLOCKQUOTE> |
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| 304 | |
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| 305 | <a name="6"></a> |
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| 306 | <h3>C.6 Results Menu</h3> |
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| 307 | <BLOCKQUOTE> |
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| 308 | This menu contains links to several GSAS and |
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| 309 | one non-GSAS (lstview) |
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| 310 | programs used for analysis of results. |
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| 311 | <DL> |
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| 312 | <DT>bijcalc<DD>Thermal parameter analysis |
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| 313 | <DT>disagl<DD>Distance/angle calculations |
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| 314 | <DT>disaglviewer<DD>Display results from distance/angle calculations |
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| 315 | in a graphical browser. |
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| 316 | <DT>reflist<DD>List reflection data |
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| 317 | <DT>geometry<DD>Molecular geometry calculations |
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| 318 | <DT>hstdmp<DD>List powder histogram data |
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| 319 | <DT>istats<DD>HKL Intensity statistics |
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| 320 | <DT>rcalc<DD>Compute reflection resuduals |
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| 321 | <DT>composition<DD>Computes the chemical composition of a unit cell |
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| 322 | accounting for site multiplicies and occupancies |
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| 323 | <DT>lstview<DD>Create a box with scrollbars containing the current .LST file |
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| 324 | <DT>ramafit<DD>Fits torsion angle distributions, particularly in peptide |
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| 325 | chains, for use in restraints. |
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| 326 | <DT>seqplot<DD>Plot results from seqgsas |
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| 327 | </DL> |
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| 328 | <img SRC="m6.gif" BORDER=3 alt="EXPGUI Screen snapshot"> |
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| 329 | </BLOCKQUOTE> |
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| 330 | |
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| 331 | <a name="7"></a> |
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| 332 | <h3>C.7 Calculations Menu</h3> |
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| 333 | <BLOCKQUOTE> |
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| 334 | This menu contains programs for useful crystallographic computations. |
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| 335 | <DL> |
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| 336 | <DT>cllchg<DD>Transform unit cell |
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| 337 | <DT>composition<DD>Computes the chemical composition of a unit cell |
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| 338 | accounting for site multiplicies and occupancies |
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| 339 | <DT>rducll<DD>Unit cell reduction |
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| 340 | <DT>spcgroup<DD>Space group symbol interpreter |
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| 341 | <DT>seqgsas<DD>Invokes the sequential GSAS refinement program to run |
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| 342 | GENLES on a set of very similar data files. |
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| 343 | <DT>seqplot<DD>Plot results from seqgsas |
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| 344 | <DT>unimol<DD>Unique molecule assembler |
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| 345 | </DL> |
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| 346 | <img SRC="m7.gif" BORDER=3 alt="EXPGUI Screen snapshot"> |
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| 347 | </BLOCKQUOTE> |
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| 348 | |
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| 349 | <a name="9"></a> |
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| 350 | <h3>C.8 Macro Menu |
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| 351 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
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| 352 | </h3> |
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| 353 | <BLOCKQUOTE> |
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| 354 | The macro capability allows actions performed in EXPGUI to be captured into a |
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| 355 | file as a series of Tcl command. |
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| 356 | It is then possible to repeat the actions in a macro repeatedly |
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| 357 | by replaying the macro. Note that macro files can be edited and |
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| 358 | Tcl/Tk commands can be added to the macros to expand capabilities. |
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| 359 | As an example, this code |
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| 360 | <blockquote><TT><PRE> |
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| 361 | runAddHist Data.raw 11BM-12D.INS 1 1 T 59.9995 |
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| 362 | runAddHist Data.raw 11BM-12D.INS 2 2 T 57.9995 |
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| 363 | runAddHist Data.raw 11BM-12D.INS 3 3 T 55.9995 |
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| 364 | runAddHist Data.raw 11BM-12D.INS 4 4 T 53.9995 |
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| 365 | </PRE></TT></blockquote> |
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| 366 | can be modified to prompt for a file name and then use it in a macro: |
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| 367 | <blockquote><TT><PRE> |
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| 368 | set DataFile [tk_getOpenFile -defaultextension .raw] |
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| 369 | runAddHist $DataFile 11BM-12D.INS 1 1 T 59.9995 |
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| 370 | runAddHist $DataFile 11BM-12D.INS 2 2 T 57.9995 |
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| 371 | runAddHist $DataFile 11BM-12D.INS 3 3 T 55.9995 |
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| 372 | runAddHist $DataFile 11BM-12D.INS 4 4 T 53.9995 |
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| 373 | </blockquote></TT></DL> |
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| 374 | <DL> |
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| 375 | <DT>Record EXPGUI macro<DD> |
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| 376 | When this option is turned on, subsequent actions are recorded into the |
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| 377 | selected macro file. |
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| 378 | <DT>Add comment to macro<DD> |
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| 379 | If this option is selected, a window is opened where a string can be typed. |
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| 380 | This information is then entered at the current point within the macro file |
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| 381 | as a comment. |
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| 382 | <DT>Replay macro line-at-a-time<DD> |
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| 383 | When this option is used, a macro file is selected by the user; the |
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| 384 | contents of the macro file is displayed, and button can be pressed to execute |
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| 385 | each command in the macro file. By clicking on a line in a macro file, that line |
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| 386 | will be the next to be run, so that sections of the file can be skipped over |
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| 387 | or repeated. The macro can also be edited within the file viewer window. |
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| 388 | <DT>Replay macro all at once<DD> |
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| 389 | When this option is used, a macro file is selected by the user, and then |
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| 390 | all commands in the macro file are executed. A status window is opened that |
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| 391 | shows the number of refinement cycles, Chi<sup>2</sup> and the last sum of |
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| 392 | shifts and also allows macros to be aborted. Note that any GSAS run in progress |
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| 393 | will run to completion before the Abort is invoked. |
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| 394 | Note that <A href="#Autoupdate">Autoload EXP</A> is temporarily set to |
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| 395 | on and <A href="#execprompt">Prompt after GSAS run</A> |
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| 396 | is temporarily set to off, when this command is invoked, so that the macro |
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| 397 | runs without need for prompts. |
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| 398 | |
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| 399 | <DT>Show GSAS output in window<DD> |
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| 400 | When this option is selected, GSAS programs are run in a separate window |
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| 401 | that is created for each program run -- even during macro execution. |
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| 402 | When this option is deselected, output from GSAS programs is placed in a |
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| 403 | separate file |
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| 404 | (<I>XXXXXXXX</I>_mac.LST where <I>XXXXXXXX</I> is the experiment name) |
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| 405 | and LSTVIEW is opened to view the output from that .LST file. |
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| 406 | </DL> |
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| 407 | </BLOCKQUOTE> |
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| 408 | |
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| 409 | <a name="8"></a> |
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| 410 | <h3>C.9 Import/Export Menu</h3> |
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| 411 | <BLOCKQUOTE> |
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| 412 | This menu contains utilities for importing information into GSAS and |
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| 413 | exporting it to other programs. |
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| 414 | <DL> |
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| 415 | <DT>Coord Export<DD>This provides a series of routines that are used |
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| 416 | to write coordinates and possibly other information to files:<P> |
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| 417 | <DL> |
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| 418 | <DT>gsas2cif<DD>Prepares IUCr crystallographic information (CIF) file |
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| 419 | that documents the current refinement. The CIF contains the |
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| 420 | coordinates for all phases as well as the observed and computed |
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| 421 | diffraction patterns. The templates used by GSAS2CIF can be customized |
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| 422 | to provide a detailed description of the experimental measurements and |
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| 423 | results for use in documenting analysis for publication or |
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| 424 | deposition. |
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| 425 | <DT>coords-only CIF<DD>For export of intermediate results to another |
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| 426 | program, CIF can be a useful exchange format. This routine provides a |
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| 427 | CIF with the current coordinates from one phase and not much else. |
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| 428 | <a name="DRAWxtl"></a> |
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| 429 | <DT>export to DRAWxtl<DD> |
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| 430 | <A HREF="http://www.lwfinger.net/drawxtl/">DRAWxtl</A> |
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| 431 | is a very useful free program for display of structures and |
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| 432 | maps. This writes a .STR input file used in the DRAWxtl |
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| 433 | program and optionally launches DRAWxtl, if installed. |
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| 434 | While the control options offered by EXPGUI are relatively |
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| 435 | modest (display of polyhedra, |
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| 436 | selection for bonds to be drawn, display of Fourier contours), |
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| 437 | once the DRAWxtl program is launched, the full range of DRAWxtl |
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| 438 | options can be accessed from that program's GUI. When a Fourier map |
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| 439 | contour is included, the Fourier parameters are set, the map is |
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| 440 | computed (program fourier) and is converted to the format needed by |
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| 441 | DRAWxtl (program gsas2map) automatically. |
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| 442 | <DT>export to SHELX<DD>This writes coordinates for a selected phase in |
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| 443 | the .INS format used by SHELX and several other programs. |
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| 444 | <DT>export to PLATON<DD>This writes coordinates for a selected phase in |
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| 445 | the .SPF format used by PLATON |
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| 446 | <DT>export test format<DD>This demonstrates how a coordinate export |
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| 447 | routine can be added to EXPGUI. See the <A |
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| 448 | HREF="expgui_cfg.html#export">documentation on this</A> for further |
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| 449 | information. |
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| 450 | <DT>export to FOX<DD>This prepares a XML file with coordinates for use |
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| 451 | in the FOX program |
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| 452 | <DT>MSI .xtl<DD>Prepare a .XTL format file of atomic positions. This |
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| 453 | file is used in older Accelrys software such as Cerius and |
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| 454 | Insight-II. It may no longer be of value. |
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| 455 | </DL> |
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| 456 | |
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| 457 | <DT>CIF Export<DD>This provides a series of routines that are used |
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| 458 | to prepare CIF files:<P> |
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| 459 | <DL> |
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| 460 | <DT>gsas2cif<DD>Prepares IUCr crystallographic information (CIF) file |
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| 461 | that documents the current refinement. The CIF contains the |
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| 462 | coordinates for all phases as well as the observed and computed |
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| 463 | diffraction patterns. The templates used by GSAS2CIF can be customized |
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| 464 | to provide a detailed description of the experimental measurements and |
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| 465 | results for use in documenting analysis for publication or |
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| 466 | deposition. |
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| 467 | <DT>FillTemplate<DD>Used to edit the CIF template files used in GSAS2CIF |
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| 468 | <DT>CIFselect<DD>Used to select interatomic distances and angles to be |
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| 469 | included in the CIF created by GSAS2CIF. |
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| 470 | </DL> |
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| 471 | |
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| 472 | <DT>hklsort<DD>Prepare HKL tables |
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| 473 | <DT>pubtable<DD>Prepare atom parameter tables |
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| 474 | <DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse) |
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| 475 | <DT>cad4rd<DD>Prepare CAD4 single crystal data |
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| 476 | <DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format |
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| 477 | <DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b |
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| 478 | <DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data |
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| 479 | <DT>sxtldata<DD>Prepare generic single crystal data |
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| 480 | <DT>gsas2pdb<DD> |
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| 481 | Import (using GSAS2PDB & EXPEDT) and export coordinates (for |
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| 482 | macromolecular phases) to/from Protein Data Base files |
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| 483 | <DT>ref2asc<DD> |
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| 484 | Exports a GSAS reflection file to ASCII for use in non-GSAS programs |
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| 485 | <DT>ref2bin<DD> |
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| 486 | Imports an ASCII reflection file to the GSAS binary format |
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| 487 | <DT>gsas2map<DD>Exports a Fourier map in formats used by other |
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| 488 | programs (for example Fox and DRAWxtl). |
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| 489 | </DL> |
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| 490 | <img SRC="m8.gif" BORDER=3 alt="EXPGUI Screen snapshot"> |
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| 491 | </BLOCKQUOTE> |
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| 492 | |
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| 493 | <hr> |
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| 494 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
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| 495 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
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| 496 | </TH><TH><A Href="liveplot.html">Next page<BR>(Utilities)</A> |
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| 497 | </TH><TH><A Href="expgui7.html">Previous page</A> |
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| 498 | </TH></TR></TABLE> |
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| 499 | |
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| 500 | <P> |
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| 501 | <font size=-1><? lastmod(); ?> </font> |
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| 502 | <br> |
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| 503 | $Revision: 1225 $ $Date: 2012-11-08 19:42:25 +0000 (Thu, 08 Nov 2012) $ |
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| 504 | </blockquote> |
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| 505 | </body> |
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| 506 | </html> |
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