DirAx Examples
The examples 1-4 are those given in the paper.
The actual results may be slightly different (notably for example1)
due to modifications in program details.
Only user input is shown in the Examples.
! note:
! these are comment lines,
! do not type.
Use the command example 'n' to read example data.
You can run all the examples in one command:
dirax < ex_solutions.inp > ex.out
and compare the results with the file ex_solutions.out.
0 straightforward
1 fragmented crystal
2 area detector small protein
3 incommensurate crystal
4 one axis much longer
5 twinned crystal
6 inaccurate data
7 not accurate and large cell
8 twin crystal and ill-distributed data
9 twinned crystal
10 area detector data protein
11 two lattices
12 twin. Two solutions in one run
ex00 - This is a straightforward model run for a single lattice. (In fact
too easy for DirAx.)
dirax |
! start program |
example 0 |
! read ex00.drx |
go |
! run with defaults |
lo |
! accept proposed ACL and show H indices |
ro |
! show cell and [R] and [D] matrices |
write |
! write file ex00.out for print-out |
end |
! finish program |
Note: without end DirAx remains active and you may continue
with other DirAx commands, e.g. read filename, example nn.
If appropriate, use default to reset all
parameters before a next go.
This example is also presented in the DirAx Course.
ex01 - Data from a fragmented crystal. First run with default parameters
and accept proposed solution. Inspect the hkl list and note that more
reflections could be made fitting with a wider IndexFit: change
value to 6 and select the default solution.
dirax |
! |
example 1 |
! data from a fragmented crystal |
list |
! show input data |
go |
! run with defaults |
lo |
! note that some refl's might fit with... |
indexfit 6 |
! ...a more relaxed fitting criterion |
acl |
! display solutions with new parameters |
auto |
! select solution with most H refl's |
lch invert |
! interchange n <--> H |
go |
! go again with n-refl's only, for other lattice |
end |
! |
The alien reflections do not form one lattice and cannot be
identified properly.
ex02 - Area detector data for a small protein, note narrow phiB region.
Set Dmax to 160. The crystal is known to be tetragonal, so there IS
something wrong with the data(conversion)!
dirax |
! |
example 2 |
! area detector data for a small protein |
dmax |
! display current dmax |
160 |
! dmax set larger than usual |
go |
! |
lo |
! list H and n refls |
write |
! |
end |
! |
You might try the default dmax = 80 and see what happens.
ex03 - Data from an incommensurate crystal from dr. J.L. de Boer,
Groningen. As usual these are very accurate data (from SET4 procedure on
CAD4). We know that problems might be ahead so we set LevelFit to 1/3000
(more severe criterion) to discriminate interfering reflections.
Note that super solutions are found with (almost) all reflections fitting.
We know however (aha!) that the correct volume is about 100 so we select
the appropriate ACL. In the hkl list you see that not fitting reflections
are at discrete distances from main lattice points.
dirax example 3 |
! data from an incommensurate crystal |
go |
! run with defaults |
acl auto |
! first accept 'best' solution |
loh |
! list fitting reflections |
acl 16 |
! now overrule superlattice (*) |
loh |
! list fitting refl's (x) |
lon |
! list satellite refl's |
end |
! |
(*) Note that for this solution alpha = gamma = 90 and a = c,
so it is worth trying it. (Moreover the cell volume was expected
to be about 100)
(x) Note the extremely small errors (1/err): SET4 data from
dr Jan L. de Boer, Groningen, NL.
ex04 - One axis much longer than the others (more than 80 A), a classic
indexing problem. Set Dmax to 120 (200 will work too, not critical if
large enough).
dirax |
! one axis much longer than the others,.. |
example 4 |
! ...a classic indexing problem. |
dmax 120 |
! increase dmax |
go |
! for the rest use defaults |
lo |
! inspect list |
end |
! |
ex05 - Data from a twinned crystal. Default parameters. A super solution
is found for all reflections, which is common with real twins.
Note: It it not possible to give general rules for this sort of problems.
The super cell COULD be correct (and IS geometrically!) but you have to
consider crystallographical aspects. Here we select ACL 18 because this
looks promising. Write results to file ex05.out1.
Continue with 'n' (not fitting) reflections only. Now the other lattice
is found. Write to file ex05.out2 and compare with .out1 later.
Normally with so few 'n' reflections a sub-lattice is found rather then a
congruent lattice. Then you have to search further selectively.
dirax |
! |
example 5 |
! data from a twinned crystal |
go |
! run with defaults |
acl 18 |
! overrule super lattice solution ACL 25 |
go |
! go again with H-refl's only, for 1st lattice |
cell |
! cell etc. for 1st lattice |
store a |
! save this solution |
write ex05.out1 |
! write file for print-out |
lch |
! |
invert |
! H -> n and n -> H |
go |
! again with N-refls only, for other lattice |
loh |
! list H refls for 2nd lattice |
cell |
! cell etc. for 2nd lattice |
store b |