Changeset 5483 for trunk/help
- Timestamp:
- Jan 29, 2023 5:03:24 PM (2 years ago)
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- 1 edited
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trunk/help/gsasII-phase.html (modified) (3 diffs)
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TabularUnified trunk/help/gsasII-phase.html ¶
r5317 r5483 3629 3629 for this phase. </span></p> 3630 3630 3631 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo4'><![if !supportLists]><span 3632 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family: 3633 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> 3634 </span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Fourier 3635 map - </span></b><span style='mso-fareast-font-family:"Times New Roman"'>compute 3636 Fourier maps according to the controls set at bottom of General page.<o:p></o:p></span></p> 3637 3638 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo4'><![if !supportLists]><span 3639 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family: 3640 Symbol;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>·<span 3641 style='font:7.0pt "Times New Roman"'> 3642 </span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Search 3643 map - </span></b><span style='mso-fareast-font-family:"Times New Roman"'>search 3631 <UL><DL> 3632 <DT><B>Fourier map 3633 </B></DT><DD>Compute Fourier maps according to the controls set at 3634 bottom of General page. 3635 </DD><P></P> 3636 3637 <DT><B>Search map 3638 </B></DT><DD>Search 3644 3639 the computed Fourier map. Peaks that are above ‘Peak cutoff’ % of the maximum 3645 3640 will be found in this procedure; they will be printed on the console and will 3646 3641 be shown in the ‘<a href="#Phase-Map_peaks">Map peaks</a>’ page. This page will 3647 3642 immediately be shown, and the peaks will be shown on the structure drawing for 3648 this phase as white 3-D crosses.<b><o:p></o:p></b></span></p> 3649 3650 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo4'><![if !supportLists]><span 3651 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family: 3652 Symbol;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>·<span 3653 style='font:7.0pt "Times New Roman"'> 3654 </span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Charge 3655 flipping - </span></b><span style='mso-fareast-font-family:"Times New Roman"'>This 3656 performs a charge flipping <i style='mso-bidi-font-style:normal'>ab initio</i> 3643 this phase as white 3-D crosses. 3644 </DD><P></P> 3645 3646 <DT><B>Charge flipping 3647 </B></DT><DD>Performs a charge flipping <i style='mso-bidi-font-style:normal'>ab initio</i> 3657 3648 structure solution using the method of <span class=SpellE>Oszlanyi</span> & 3658 3649 <span class=SpellE>Suto</span> (Acta <span class=SpellE>Cryst</span>. A60, 134-141, … … 3674 3665 the resulting phases; the map could be still offset by a few steps), searched 3675 3666 for peaks and the display shifts to <b style='mso-bidi-font-weight:normal'>Map 3676 peaks</b> to show them.<b><o:p></o:p></b></span></p> 3677 3678 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo4'><![if !supportLists]><span 3679 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family: 3680 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> 3681 </span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>4D 3682 Charge flipping – </span></b><span style='mso-fareast-font-family:"Times New Roman"'>4-Dimensional<b> 3683 </b>charge flipping is done for a modulated structure.<o:p></o:p></span></p> 3684 3685 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo4'><![if !supportLists]><span 3686 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family: 3687 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> 3688 </span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Clear 3689 map -</span></b><span style='mso-fareast-font-family:"Times New Roman"'> This 3667 peaks</b> to show them. 3668 </DD><P></P> 3669 3670 <DT><B>4D Charge flipping 3671 </B></DT><DD>4-Dimensional charge flipping is done for a modulated structure. Only 3672 available for phases with a 3+1 superspace group. 3673 </DD><P></P> 3674 3675 <DT><B>Clear map 3676 </B></DT><DD>This 3690 3677 clears any Fourier/charge flip map from memory; the Fourier map controls are 3691 also cleared.<o:p></o:p></span></p> 3692 3693 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo4'><![if !supportLists]><span 3694 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family: 3695 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> 3696 </span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>MC/SA</span></b><span 3697 style='mso-fareast-font-family:"Times New Roman"'> – Perform Monte 3678 also cleared. 3679 </DD><P></P> 3680 3681 <DT><B>MC/SA 3682 </B></DT><DD>Perform Monte 3698 3683 Carlo/Simulated Annealing structure solution using the model as set up in the 3699 MC/SA tab and the controls at the bottom of this tab.<o:p></o:p></span></p> 3700 3701 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo4'><![if !supportLists]><span 3702 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family: 3703 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> 3704 </span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Multi 3705 MC/SA</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 3706 Perform multiple Monte Carlo/Simulated Annealing structure solutions, 3707 accumulating the best ones as set up in the MC/SA tab.<o:p></o:p></span></p> 3708 3709 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo4'><![if !supportLists]><span 3710 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family: 3711 Symbol;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>·<span 3712 style='font:7.0pt "Times New Roman"'> 3713 </span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Transform 3714 </span></b><span style='mso-fareast-font-family:"Times New Roman"'>- This 3684 MC/SA tab and the controls at the bottom of this tab. 3685 </DD><P></P> 3686 3687 <DT><B>Multi MC/SA 3688 </B></DT><DD>Perform multiple Monte Carlo/Simulated Annealing structure solutions, 3689 accumulating the best ones as set up in the MC/SA tab. 3690 </DD><P></P> 3691 3692 <DT><B>Transform 3693 </B></DT><DD>This 3715 3694 allows for a change in axes, <span class=GramE>symmetry</span> or unit cell. It 3716 3695 is also used to create a magnetic phase from a chemical (nuclear) phase. One 3717 3696 important transformation that can be done here is for Origin 1 settings to 3718 Origin 2 (<a href="#_Origin_1_->">described below</a>).<b><o:p></o:p></b></span></p> 3719 3720 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo4'><![if !supportLists]><span 3721 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family: 3722 Symbol;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>·<span 3723 style='font:7.0pt "Times New Roman"'> 3724 </span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Compare 3725 – </span></b><span style='mso-fareast-font-family:"Times New Roman"'>Compares 3697 Origin 2 (<a href="#_Origin_1_->">described below</a>). 3698 </DD><P></P> 3699 3700 <DT><B>Compare Cells 3701 </B></DT><DD>Compares 3702 two supplied unit cells for a transformation matrix that converts one 3703 to the other within supplied search tolerances using the NIST*LATTICE 3704 program. If this is used, please cite: 3705 <UL> 3706 <LI>V. L. Karen and A. D. Mighell, NIST Technical Note 1290 (1991). 3707 <A HREF="https://nvlpubs.nist.gov/nistpubs/Legacy/TN/nbstechnicalnote1290.pdf">(link)</A> 3708 <LI>V. L. Karen & A. D. Mighell, U.S. Patent 5,235,523. 3709 <A HREF="https://patents.google.com/patent/US5235523A/en?oq=5235523">(link)</A> 3710 </UL> 3711 </DD><P></P> 3712 3713 <DT><B>Compare polyhedra 3714 </B></DT><DD>Compares 3726 3715 idealized <span class=SpellE>polyhedra</span> (tetrahedron & octahedron) to 3727 those obtained from a Reverse Monte Carlo run in RMCProfile.<b><o:p></o:p></b></span></p> 3728 3729 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo4'><![if !supportLists]><span 3730 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family: 3731 Symbol;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>·<span 3732 style='font:7.0pt "Times New Roman"'> 3733 </span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Select 3734 magnetic/subgroup phase – </span></b><span style='mso-fareast-font-family:"Times New Roman"'>allows 3735 selection of the results from a magnetic subgroup analysis done in the 3716 those obtained from a Reverse Monte Carlo run in RMCProfile. 3717 </DD><P></P> 3718 3719 <DT><B>Select magnetic/subgroup phase 3720 </B></DT><DD>Selection of the results from a magnetic subgroup analysis done in the 3736 3721 Phase/Unit cells list tab. This will generate a new magnetic phase. Can also be 3737 3722 used to select from possible subgroups of a nonmagnetic super group for 3738 3723 possible symmetry reduction. See <a href="gsasII-pwdr.html#PWDR_Unit_Cells_List">Unit 3739 cells list</a> for further information.<b><o:p></o:p></b></span></p> 3740 3741 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l9 level1 lfo4'><![if !supportLists]><span 3742 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family: 3743 Symbol;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>·<span 3744 style='font:7.0pt "Times New Roman"'> 3745 </span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Protein 3746 quality</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 3747 evaluate protein quality by python versions of <span class=SpellE>errat</span> 3724 cells list</a> for further information. 3725 </DD><P></P> 3726 3727 <DT><B>Protein quality 3728 </B></DT><DD>Evaluate protein quality by python versions of <span class=SpellE>errat</span> 3748 3729 & errat2 codes by <span class=SpellE>Colovos</span>, C. & <span 3749 class=SpellE>Yeates</span>, T.O. Protein Science 2, 1511-1519 (1991).<b><o:p></o:p></b></span></p> 3730 class=SpellE>Yeates</span>, T.O. Protein Science 2, 1511-1519 (1991). 3731 </DD><P></P> 3732 </DL></UL> 3750 3733 3751 3734 <p class=MsoNormal><span class=MsoHyperlink><span style='color:windowtext; … … 7519 7502 </span></div> 7520 7503 7521 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><!-- hhmts start -->Last modified: Wed Jul 27 15:05:57 CDT 2022<!-- hhmts end --><o:p></o:p></span></p>7504 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><!-- hhmts start -->Last modified: Sun Jan 29 17:50:46 CST 2023 <!-- hhmts end --><o:p></o:p></span></p> 7522 7505 7523 7506 </div>
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