The platon crystallographic package - səhifə 34
Molecules on symmetry elements are completed with symmetry related parts. This process
may lead to large clusters of ARU's in the case of polymeric structures. Clicking on the
Join-Expand(Changing from RED to White) will minimize the number of
ARU's generated in the connectivity search for polymeric structures. Note: Atoms unwanted
in a subsequent ORTEP plot can be removed with the
DeleteAtomsbutton on the ORTEP
184.108.40.206 - ORGANIC/INORGANIC Toggle
Different default Radii sets are used for Organic and Inorganic structures respectively. This
option is in particular useful for coordination complexes. No ring search is done by default
for inorganic structures. The default setting is triggered by the presence or absence of an
organic carbon atom (i.e. C & H present). Example: The default for NaCl will be
whereas organometallic compounds are treated as
organic. This will avoid the generation of
infinite structures as part of the connectivity search.
220.127.116.11 - ROUND
By default, coordinates and derived data (bonds, angles etc.) are rounded following the
established 1-19 rule (This is the Acta Crystallographica standard and requirement).
This default can be changed by clicking in one of the alternative boxes
- leftmost box - no rounding i.e. ROUND OFF
- second box - round following the 1-9 rule
- third box - round following the 1-19 rule [default].
rightmost box - round following 1-29 rule
18.104.22.168 - Parentheses Toggle
By default, the numerical part of the label is enclosed in parentheses in listing files but not
in ORTEP and PLUTON plots. The latter is controlled in the respective sub-menus.
22.214.171.124 - Label-Alias Toggle
PLATON sets some restrictions on atom labels. Reasons are partially historical (to save
memory space) but also the fact that a label is interpreted in terms of atom type and
symmetry extension and the need for condensed geometry listings. When a label is given in
a CIF that conflicts with those rules, an alias (terminated with a #) is generated. By default,
the original labels are presented on output and graphics where ever possible. With this
toggle ON (RED), the aliases used in PLATON are given.
R/S-Determination is enforced when active (RED). Otherwise it is at the program to decide. The
current algorithm for the R/S determination works well with most structures. However, there can be
problems with chiral atoms that are part of complex interconnected ring systems. Also there may be
problems when (rare) cis/trans special rules should have been applied.
NORM H-BOND Toggle
X-H (X = B, SI, C, O, N) distances are normalized to standard values when the toggle is
ON. Default target values (That can be changed with prior 'SET PAR' instructions are:
- B-H, PAR(294) = 1.19
- SI-H, PAR(295) = 1.50
- C-H, PAR(296) = 1.083
- N-H, PAR(297) = 1.009
- O-H, PAR(298) = 0.983
126.96.36.199 - NOSYMM Toggle
When this option is active (i.e. shown RED), no symmetry expansion is done as part of the
connectivity set-up. This toggle has effect only when activated before any explicit or
implied CALC INTRA instruction is executed. No symmetry expansion can be useful when
the application of symmetry relations results into undesired infinite networks in the
subsequent analysis (useful for atom renaming etc.). Similarly, undesired infinite chain
expansion is avoided in the ORTEP display.
Toggle for the (NOT) DISPLAY of major/minor disorder (e.g. in ORTEP). Clicking in the
left box invokes the major disorder form and clicking in the right box invokes the minor
disorder form. Clicking again in the same box give the complete structure back.
188.8.131.52 - LIST ARU/RCELL
Clicking in in the left box lists the asymmetric residue codes (ARU) on the display. This is
generally meaningful only after some CALC instructions since the default ARU 1555 is not
shown. Clicking in the right box will list reciprocal cell dimensions in the message window
at the bottom of the display.
184.108.40.206 - LIST CELL/SYMMETRY
Clicking in the left box lists the cell dimensions in the message window at the bottom of the
display. Clicking in the right box will display the symmetry details of the current space
group (equivalent with the keyboard instruction
LIST SYMM) on the Graphics Window for
220.127.116.11 - LIST ATOMS
Clicking on LIST ATOMS (equivalent to the keyboard instruction
LIST ATOMS) displays the
current coordinate data along with info about population parameters and whether the atom has been
moved on the Graphics Window for inspection.
18.104.22.168 - LIST BONDS
Clicking on LIST BONDS (equivalent to the keyboard instruction
LIST BONDS) will
display the current connectivity table on the terminal Window.
22.214.171.124 - LIST FLAGS & RADII
Clicking in the left box is equivalent to the keyboard instruction
LIST FLAGSwill list the
values of various flags associated with atoms
. Clicking in the right box is equivalent to the
LIST RADII(Covalent & van der Waals) on the graphics window for
inspection. The default van der Waals radii may be customized with the SET VDWR
SET VDWR Cu .73 O 1.38
126.96.36.199 - EXCLUDE H Toggle
This will EXCLUDE all H-atoms from the analysis. (to be issued before any other
instruction or after a RESET). This feature may be useful in combination with a CSD search
in case that the H atoms are dubious.
188.8.131.52 - MinPeakHgt
The click position determines the minimum peak hight of Q-peaks for inclusion. Choices are: 0.2,
0.4, 0.6, 0.8, 1.0 e/Angstrom^3. The default is 0.4 e/Angstrom^3. The current value is displayed in
the message window at the bottom of the display. This option is meaningful for molecular display
only. Note: A global parameter value is set that is not returned to its default value with a RESET
184.108.40.206 - MinPeaksDis
The click position determines, as an inclusion criterium, the minimum distance of a Q-peak
to the other atoms. Choices are: 0.0, 0.25, 0.50, 0.75, 1.0 Angstrom. The default value is 0.5
Angstrom. The current value is displayed in the message window at the bottom of the
display. This option is meaningful for molecular display only. Note: A global parameter
value is set that is not returned to its default value with a RESET instruction.
220.127.116.11 – Q-Peak-Incl Toggle
Option to include residual density 'Q-Peaks' from the SHELXL '.
res' file that are stored
beyond the HKLF line. The left box is an on/off toggle. Alternatively, clicking in the right
box sets the option on (RED). This option is meaningful for molecular display only.
18.104.22.168 - KeyInstructionList Toggle
This button will give an on-screen listing of the available keyboard instructions. Clicking on
END will bring the PLATON main menu back.
22.214.171.124 - PREV/NEXT Toggle
Toggle to return to the previous entry or proceed to the next entry on a multi-entry CIF or
afs -> Meningoensefalit, meningoensefalit
afs -> Nb deze bovenstaande tekst wel weghalen!
afs -> Allergen Checklist for Food Suppliers or Manufacturers
Dostları ilə paylaş:
©2018 Учебные документы
Рады что Вы стали частью нашего образовательного сообщества.