The platon crystallographic package - səhifə 40
order to refine the
correct absolute structure as indicated by the Flack parameter. Inversion
may include change of space group when enantiomeric space group pairs
are involved or require special origin shifts. Clicking on the INVRT button
will arrange for inversion of the structure in the next
SHELXL refinement cycles by setting up the proper parameters for the
When change of space group is implied, e.g. P31 to P32, conversion to (creation of) the new
space group is arranged automatically.
Enantiomorphic space group pairs are:
[P41, P43], [P4122, P4322], [P41212, P43212], [P31, P32], [P3121, P3221], [P3112, P3212
], [P61, P65], [P62, P64], [P6122, P6522], [P6222, P6422], [P4132, P4332]
Space groups requiring an origin shift
Fdd2, I41, I4122, I41md, I41cd, I-42d, F4132
HFREE: Release all AFIX constraints set with HFIX. This allows for the refinement of
previously fixed positional parameters.
126.96.36.199 - ASYM & VIEW
ASYM: Clicking in the left box will generate an averaged reflection set for the current
symmetry with systematic extinctions removed. See
for more details.
VIEW:Clicking in the right box will invoke the display of the reciprocal lattice in order to
inspect for data quality and completeness. See
for more details.
188.8.131.52 - SQUEEZE & FCF
for details on SQUEEZE
SQUEEZE: Clicking in this box will initiate a 'SQUEEZE' calculation.
Conditions for use of SQUEEZE are:
- There should be voids in the structure (This can be tested with the SOLV option).
- Adequate correction for absorption.
- Prior refinement should be done with the best possible model (i.e. Anisotropic
parameters for the non-hydrogen atoms in the ordered part of the structure and all
hydrogen atoms attached to the model included). Disorder sites may have been included
with dummy atoms.
All disorder sites should be deleted prior to the SQUEEZE run.
FCF:Add solvent contribution to the SHELXL produce FCF to produce an FCF based on
the original reflection intensities.
184.108.40.206 - ADDSYM & SOLV
This Menu entry provides easy access to two PLATON functions operated on the current
's.res'. Subsequently, 'ghostview' is invoked for inspection of the generated listing file.
ADDSYM:Clicking on ADDSYM invokes the S-instruction 'PLATON ADDSYM'. The
current 's.res' is checked for potential (missed) higher symmetry. Reported new (missed)
symmetry is displayed in RED preceded by M/P. Transfer to the suggested space group
can be accomplished by clicking on TRMX. The relevant alternative directories and
links are setup automatically. The new (adapted) .res is copied as well.
SOLV:Clicking on SOLV invokes the S-instruction 'CALC SOLV'. The current 's.res' is
checked for 'solvent accessible areas', possibly indicating missed (disordered)
220.127.116.11 - VALIDATION & REPORT
VALIDATION: Clicking in the left box invokes a CIF-Validation run in order to detect
possible problems with the current analysis.
for more details.
REPORT: Clicking in the right box should generate a report on the current structure
for more details.
18.104.22.168 - AutoRenum
Atoms are automatically renamed based on a network topology reated algorithm.
22.214.171.124 - SKIP or ACCEPT-DEFAULT
ACCEPTconfirms the suggested default instruction or datum suggested in .
SKIPwill skip the currently suggested next instruction (when applicable) and
move to the next suggested instruction.
Currently implemented SKIP operations are implemented for ABSPSI & DELABS. In all
other cases, clicking on SKIP will have no effect on the flow of the calculations.
1.4.18 – SYSTEM_S SUB-MENU #1
126.96.36.199 - LOG & RELINK – History Functions
LOGinstruction provides a history log of previous actions on the current compound. In
particular, it documents where earlier results are stored and where they can be recovered
The numerical code hh/kkk/nnn indicates:
- hh- Number of the TRansformation MatriX choosen in the TRMX stage.
New selections may be made with the TRMX instruction.
- kkk- SpaceGroup number selected in the SPGR stage.
New selections (within the current TRMX selection) may be done with the SPGR
- nnn- Link state identifier.
May be manipulated with the RELINK instruction.
RELINKinstruction resets the current context (i.e. .res and .hkl) to a previous context.
However note: only the most recent version of the correction for absorption of a given type
(abspsi, abstompa etc) is retained. Older results are overwritten in the subdirectories
corresponding to the correction for absorption at hand. Clicking on RELINK without a
numerical value will go to the previous context (middle box) or a more recent context (right
box). RELINK nnn, will link to the requested hh/kkk/nnn context.
188.8.131.52 - TREE & LIST
TREE:The TREE instruction provides a listing of all relevant files, directories and current
links for the current compound.
LIST:The LIST instruction gives an overview of current status and parameter values.
When relevant, beyond 'Rav' both R(aver) before and after absorption correction is displayed.
184.108.40.206 - RemoveTree
220.127.116.11 – XtalDisplay.
Display of the crystal based on a set of bounding faces. This option may be useful for
checking a face set before attempting numerical absorption correction.
18.104.22.168 - CELL & HELENA
CELL:This the first instruction in the start-up sequence of a new compound related
CELL dimensions (and wavelength) may be accepted as suggested or adapted.
HELENA:The program HELENA may be invoked for the reduction of CAD4 data into a
standard shelx.hkl file (including direction cosines).
22.214.171.124 - FLIPPER
(to be done)
126.96.36.199 - SinTHeta/Lambda-max
Button boxes for limiting the data set resolution during SHELXL refinement.
Sin(Theta/Lambda)-max levels 0.54, 0.60, 0.65, 1.0 corresponding to theta-max (MoKa)
22.5, 25.0, 27.5, max Degrees.
188.8.131.52 - ORGANIC
184.108.40.206 – VOID-CHECK Toggle
Toggle for automatic checking for solvent accessible areas in the structure.
220.127.116.11 – ADDSYM-CHECK Toggle
Toggle to set for checking for missed & pseudo symmetry at appropriate stages of the
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