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Should DIFABS be Banned?
Discussion on sci.techniques.xtallography
(20th April 1994 to 3rd May 1994 - and beyond (18th November 1999)
Latest Update - 18th November 1999
Using DIFABS in Crystals as a diagnostic test
Why bother using DIFABS Analysis?
"You can use DIFABS in test mode at any stage, and it quite simple tells
you if there is a systematic trend to the residual as a function of orientation.
If the plot is fairly monochrome, then the residuals are not peaking up.
If there are bright patches, it means that there is a systematic trend to
the residual. Either FO or Fc is systematically wrong. Possible reasons
are:
- Absorption
- crystal damage (bending, shearing)
- anisotropic extinction
- mis-centering
- very anisotropic 'spot' shape (selective truncation)
- Application of unsuitable/ill-measured psi correction
(Use of DIFABS in 'test' mode to un-corrected and psi-corrected
data can help display the effect of the correction more clearly than just
looking at Rint)
- We have no evidence that missing atoms (eg solvent) lead to Difabs-like
effect"
Refer:
Gui WinCRYSTALS 2000 Web and FTP sites
2nd Last Update - 6th April 1999
A Web Based Comparison of Absorption Correction Methods - using the WinGX Suite
The Initial Discussion
Creating a Summary Document of the Discussion
(Included in "L. M. D. Cranswick, J. Silverton and T. Buckner",
Global communications , IUCr Newsletter. Vol. 3, (1), 1995, pp. 6-8,10)
Where do you get the DIFABS and XABS2 software?
Comments Based on IUCr Newsletter Article (Vol. 3, (1), 1995, pp. 6-8,10)
Newsgroups: sci.techniques.xtallography
From: spea@faculty.chem.ruu.nl (Ton Spek)
Subject: DIFABS - SHOULD IT BE BANNED ??
Date: 20 Apr 94 13:43:33 GMT
Organization: Physics Department, University of Utrecht, The Netherlands
This is meant to start a (possibly heated) discussion on the use
(although according to some abuse) of the program DIFABS (Walker &
Stuart, 1983, Acta Cryst., A39, 158-166) as a method to correct for the
effects of absorption. Such a discussion is rapidly becoming acute in
view of the fact that Acta Cryst is moving to a position of strongly
discouraging the publication of structures 'massaged' with this or
similar empirical methods. A quick look through recent issues of AC-C
shows that in the order of 75% of the papers made use of empirical
correction methods .....
The arguments against DIFABS that I know of are :
- Primary data are massaged and not recoverable from the deposited
Fo/Fc-tables
- Not just absorption effects but also other systematic effects
(certainly extinction) that can be fitted with the absorption model
are polished
- Crystallographers using DIFABS are lazy.
- Hiding of all kinds of sloppy experimental practice
- Correction factor ranges are often unrealistically large
- Fudged (comfortably embellished) R-values
Supporters of DIFABS offer:
- Easy to use (once implemented as a standard procedure)
- Reliable in the hands of people who know what they are doing
- Applicable also in cases that are for various reasons inaccessable
for 'exact' correction methods.
- The only practical method for the heavily overloaded service
crystallographer.
- Experience with cases that are accessable for both correction methods
show that the results obtained with refinements based on data corrected
with both methods are nearly indistinguishable (even the ORTEP's).
so ???
Ton Spek
National Single Crystal Service Facility
Utrecht University
The Netherlands
spea@xray.chem.ruu.nl
From: "boyle@mantis.chem.unb.ca"
Newsgroups: sci.techniques.xtallography
Subject: RE: DIFABS - SHOULD IT BE BANNED ??
Date: 22 APR 94 11:08:08 AST
Organization: The University of New Brunswick
Well, Ton, I guess I'll take the bait. In general, I am against the
use of DIFABS as a routine absorption correction. I think it is bad
practice to fit the data to the model rather than fitting the model
to the data. I try to use psi scan data to make an empirical
absorption correction. While the psi scan method is not perfect, it
does have the advantage of being based on some experimental data.
One must take care that the psi scan data is not contaminated with
Renniger effects.
I'll try to address each of the arguements given below
> The arguments against DIFABS that I know of are :
>
>- Primary data are massaged and not recoverable from the deposited
> Fo/Fc-tables
I think this is a valid objection,and fits into my comment about
fitting the data to the model.
>- Not just absorption effects but also other systematic effects
> (certainly extinction) that can be fitted with the absorption model
> are polished
Some Spanish crystallographers presented a poster at a recent ACA
meeting about this. Unfortunately, I can't recall the reference at
this point. If I recall correctly, their machine had suffered a
collision and had affected the quality of the data. DIFABS
apparently did a good job of hiding these errors.
>- Crystallographers using DIFABS are lazy.
I don't think personal judgements like these are the most
appropriate criterion to apply when deciding a piece of software is
scientifically justifiable.
>- Hiding of all kinds of sloppy experimental practice
I think DIFABS has great potential for this. If there are
systematic errors in the data due to incorrectly set apetures or
other data collection parameters, these are going show up in Fobs.
The use of DIFABS assumes all systematic errors are due to
absorption, which in the above example is not the case.
>- Correction factor ranges are often unrealistically large
I can't really comment on this.
>- Fudged (comfortably embellished) R-values
I have received some pressure from my structure clients to use
DIFABS for the cosmetic improvements of R's. I have resisted such
pressure. At one time, I did do a refinement on a structure without
an absorption correction and with DIFABS. The R factor went from
0.08 to 0.05. I felt uncomfortable releasing the DIFABS refinement
(which I did not). My opinion is that if the data or model as
problems it is more honest to let these problems show up in the R
factor, ORTEP's, esd's etc. To massage the data into giving a
better R factor, is to mislead the readers of the literature
(especially non-crystallographers) about the level of confidence
they should place on the structure.
>
> Supporters of DIFABS offer:
>
>- Easy to use (once implemented as a standard procedure)
Too easy to use. I colleague once told me that he knew someone who
used DIFABS on structure where this person wanted to investigate
difference electron densities. Beacause DIFABS the data to the
model and the "standard crystallographic model" is typically
spherical atoms undergoing 3 dimensional rectilinear harmonic
motion, this person by using DIFABS was wiping out the very features
of bonding density being looked for.
>- Reliable in the hands of people who know what they are doing
Possibly. One would have to be sure that the systematic errors were
due to only absorption. Does everyone really look at each data
point collected to make sure that the scan width didn't truncate any
refections, correct apetures settings, contamination from TDS,
extinction, Renniger effects and so on? Do "overworked" service
crystallographers normally take this level of care?
>- Applicable also in cases that are for various reasons inaccessable
> for 'exact' correction methods.
This is the only reason that I would use DIFABS. If the crystal was
lost before psi scan could be taken, or if there were no suitable
refections at high enough values of chi (or kappa).
>- The only practical method for the heavily overloaded service
> crystallographer.
Is spending a couple of hours taking 3 or 4 psi scan profiles really
going to cause a bottle neck? This has not been my experience. I
spend more time checking the Laue symmetry and getting a good cell,
than I do taking psi scans.
>- Experience with cases that are accessable for both correction methods
> show that the results obtained with refinements based on data corrected
> with both methods are nearly indistinguishable (even the ORTEP's).
This is something I have wanted to test for the last couple of
years. I haven't been able to come across the right sample yet,
however. I would need a highly absorbing crystal, which contained
rigid molecules that weren't disordered. Take the data, take psi
scans, and do an exact aborption correction and compare all 3
results. I think doing a rigid body analysis on the three
structures would be informative. One could compare the values of
TLS, deltaU's, libration corrected bond lengths. I think seeing if
there is a correlation between the DIFABS 'absorption ellipsoid' and
changes in the components of the T L and S tensors derived from the
various refinements would be useful. We could answer the question
does DIFABS primarily affect the T or L tensor, or both.
As a service crystallographer, I take which samples I get and I have
not gotten a crystal which meets the above criterion. I think a
compound like SnI4 might work, but I have no facilties to prepare
compounds. Anybody want to collaborate on this?
Paul D. Boyle Dept. of Chemistry University of New Brunswick Bag
Service #45222 Fredericton, New Brunswick E3B 6E2 CANADA
boyle@mantis.chem.unb.ca
From: chem91@Elroy.UH.EDU ("Bill Harrison (713)-743-2789")
Newsgroups: sci.techniques.xtallography
Subject: Re: DIFABS - SHOULD IT BE BANNED ??
Date: 22 Apr 1994 15:12:23 GMT
Organization: University of Houston
>This is meant to start a (possibly heated) discussion on the use
>(although according to some abuse) of the program DIFABS (Walker &
>Stuart, 1983, Acta Cryst., A39, 158-166) as a method to correct for the
>effects of absorption. Such a discussion is rapidly becoming acute in
Could this be the first flame war in s.t.x? :=)
> The arguments against DIFABS that I know of are :
>
>- Primary data are massaged and not recoverable from the deposited
> Fo/Fc-tables
Good point. I guess that if DIFABS is used, then "real" Fo and
"corrected" Fo should BOTH be deposited?
>- Correction factor ranges are often unrealistically large
Good question. What *is* an acceptable correction factor range?
- for a "typical" small molecule...
- for a nasty, platy inorganic containing e.g. thallium...
>- Fudged (comfortably embellished) R-values
DIFABS can have a huge effect with inorganics -- I've seen R-factor reductions
from 15% to 5% before, and it *seems* that the anisotropic thermal parameters
are *much* more "sensible" (physically realistic) post-DIFABS. So long as you
state that DIFABS was used, I don't think it's a problem... ?
>
> Supporters of DIFABS offer:
>
>- Applicable also in cases that are for various reasons inaccessable
> for 'exact' correction methods.
Not just applicable, but perhaps essential. Most of the crystals I do
are poorly (un)faceted lumps, and an analytical correction is just not on.
I always collect psi-scan data if I can, but sometimes there just aren't
any suitable reflections, and you can't tie up the machine for another day(?)
just looking for them...
>- Experience with cases that are accessable for both correction methods
> show that the results obtained with refinements based on data corrected
> with both methods are nearly indistinguishable (even the ORTEP's).
I probably have several data sets I could test this on more systematically...
BTW, I've seen some papers which report that psi-scans *and* DIFABS were
applied...
Interesting questions!
Bill
+-------------------------------------------------------------------------+
| Bill Harrison -- University of Houston, TX -- CHEM91@JETSON.UH.EDU |
| "Only the extreme is interesting" -- Magnus Lindberg |
+-------------------------------------------------------------------------+
From: sp@oedipus.llnl.gov
Newsgroups: sci.techniques.xtallography
Subject: Re: DIFABS - SHOULD IT BE BANNED ??
Date: Fri, 22 Apr 94 15:30:52 PDT
Organization: Lawrence Livermore National Laboratory, NCD
I have not used DIFABS, but I have used XABS and XABS2 (I wrote the latter).
The program calculates a 4 dimensional scale factor from 24 coefficients
that come from Fo^2 and Fc^2 differences. Real improvements in data i.e.
the ability to find H atoms after correction for example are often quite
dramatic. Assuming DIFABS can also actually improve data, rather than just
make it closer to calculated data, and that a more rigorous technique is
not practicable, then the method is fine for routine work.
Provided that whoever applies the correction properly understands what they
are doing, and the limitations of it, then there shouldn't be a problem.
The person who wanted to use it in electron density work, for example,
shouldn't be allowed near it. Such programs have been abused in the interests
of cosmetics, however, which is unfortunate.
The 24 coefficients generated by XABS2 (12 by XABS) are currently obtained
in a standalone program. A better approach would be to refine them at the
same time as x,y,z,Uij. The least-squares process would then obtain a fit
to 'atomic parameters' and 'crystal parameters'. Then there would then be
no need to deposit data other than the dataset itself and the absorption
coefficients. Extinction is usually treated this way (and it also uses Fc in
its derivation).
Sean Parkin
Newsgroups: sci.techniques.xtallography
From: jvs@helix.nih.gov ("Jim Silverton")
Subject: Difabs
Date: Mon, 25 Apr 94 10:41:54 EDT
Organization: NIH
I must admit that my own instinctive reaction to Difabs is "CHEATING" but
is this really true? All the arguments I have seen seem to be instinctive,
stands-to-reasons or usable by "experts who know what they are doing".
Has the method ever been tested by refining data with known, introduced,
systematic errors and shown not to produce systematic errors in the
result or, even better, to increase real accuracy?
Even if the method proves harmless, it seems scientifically
unjustifiable to me to use cosmetic changes producing no real improvement
in an answer. This is especially true, as others have pointed out, if the
deposited observations have been massaged and there is no way to recall the
the raw data. I think that real, not cosmetic, improvement in the
refined structure must be demonstrated to justify the continued use of
Difabs. Preferably, tests would be done by several different laboratories
and the results compared.
James V. Silverton
NIH, Bldg. 10, Room 7N-309, Bethesda MD 20892, USA.
Phone:301.496.1515 Fax:301.402.3404
Newsgroups: sci.techniques.xtallography
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From: spea@faculty.chem.ruu.nl (Ton Spek)
Subject: Re: DIFABS - SHOULD IT BE BANNED ??
Date: 25 Apr 94 15:19:13 GMT
Organization: Physics Department, University of Utrecht, The Netherlands
"pboyle@unb.ca" writes:
>Well, Ton, I guess I'll take the bait. In general, I am against the
>use of DIFABS as a routine absorption correction. I think it is bad
>practice to fit the data to the model rather than fitting the model
>to the data. I try to use psi scan data to make an empirical
>absorption correction. While the psi scan method is not perfect, it
>does have the advantage of being based on some experimental data.
>One must take care that the psi scan data is not contaminated with
>Renniger effects.
One of the problems with psi-scan data is unfortunately: How
representative are the effects observed in individual psi-scans for
what is happening with the complete dataset (an issue well addressed
with DIFABS-type correction methods). E.g. One should be very carefull
not to use a reflection that suffers from severe extinction. As a
routine procedure we use three psi-scans to check the validity of our
absorption correction.
>Is spending a couple of hours taking 3 or 4 psi scan profiles really
>going to cause a bottle neck? This has not been my experience. I
>spend more time checking the Laue symmetry and getting a good cell,
>than I do taking psi scans.
In our automatic data collection procedure (on the CAD4), three suitable
reflections are selected 'on-the-fly' and intensites collected in 10 degree
intervals.
Ton Spek
National Single Crystal Service Facility
Utrecht University
The Netherlands
spea@xray.chem.ruu.nl
From: msrbb@csv.warwick.ac.uk (N W Alcock)
Newsgroups: sci.techniques.xtallography
Subject: Re: DIFABS - SHOULD IT BE BANNED ??
Date: 25 Apr 1994 16:44:31 +0100
Organization: University of Warwick, Coventry, UK
Some points in support of Ton Spek
1. Upper bounds can easily be set on the absorption correction range, by
assuming that the minimum and maximum T are represented by rays traversing
the shortest and longest dimensions of the crystal -
comparison with analytical corrections shows that this is a good
estimate. Some data from a couple of numbers of Acta last year for DIFABS
corrections
Mu/mm-1 Tmax/Tmin Est. range Comment
0.08 1.008 1.02 DIFABS pointless
1.05 1.2 1.37 Under-corrected
4.0 2.16 1.86 Disturbing over-correction
14.9 1.12 6.93 Very worrying
0.09 1.39 1.03 This crystallographer should go back
to school!
2. If the service crystallographer gets organised, then carrying out accurate
face-indexed measurements of the crystal need take no more than 1/2 hour -
certainly less than a good set of psi-scan measurements - and this can be done
off the diffractometer.
3. If DIFABS does anything at all, it will equalise the mean anisotropic
displacement parameters in all directions - fine (probably) if your molecule
has no significant anisotropy of motion, but not otherwise. I can see **NO**
justification for publishing thermal ellipsoid diagrams after DIFABS has been
used.
Nat Alcock
Newsgroups: sci.techniques.xtallography
From: spea@faculty.chem.ruu.nl (Ton Spek)
Subject: Re: DIFABS - SHOULD IT BE BANNED ??
Date: 25 Apr 94 19:04:57 GMT
Organization: Physics Department, University of Utrecht, The Netherlands
To be sure: my ranking of methods for absorption correction is
a - analytical (e.g. ABSPSI, XTAL etc)
b - gaussian (e.g. shelx76, XTAL, etc.)
c - difabs and similar approaches
d - sphere or cylinder approximation (when appropriate)
e - psi-scan corrections
Unfortunately, it is only in the case 'd-sphere' that part of the
original data may be recovered (given the radius of the sphere) from
the Fo/Fc tables.
Some of the problems I see with methods a & b are:
- They can be used in a very sloppy empirical way as well on the
basis of guestimates of the bounding planes.
- How can one (i.e. a referee) be sure that the faces have
been indexed correctly ?
Our way to address such problems is to collect and correct additional
psi-scan data and analyze their residual intensity fluctuation after
correction. Wrong indexing is easily recognized in this way in the form
of a correction (as a function of psi) that is out of phase. A similar
test can be put in place for empirical correction techniques as well.
I am still hoping that somebody will come up with a nice gadget
(preferably) on my diffractometer telling me what my nice cut-to-size
oil-covered air-sensitive crystal approximates to in terms of h,k,l &
d's..... Up to then it is very tempting to give DIFABS a try ... or
can/should we persuade our customers to generate 'journal-quality' as
opposed to 'xray-quality' crystals...sothat it is worth the effort to
do an exact correction... Programs and computing time are no problem:
An analytical correction and a DIFABS run both take only in the order
of minutes on my workstation...
What would be realy interesting is when somebody could come up with a
goodlooking structure (in terms of the highly valued R-factor) that
nonetheless is wrong (geometry etc) due to the application of DIFABS.
In summary: in our setup: standard low-temperature with inert oil covering
the air sensitive crystal, DIFABS does a very efficient job in providing
the synthetic chemists with an answer (including in many cases hydrogen
atom positions picked up from a difference map) as long as deformation
densities are not the issue.
Ton Spek
From: geib+@pitt.edu (Steven Geib)
Newsgroups: sci.techniques.xtallography
Subject: BANNING OF DIFABS
Date: 25 Apr 94 19:56:46 GMT
Organization: University of Pittsburgh
I'm not sure who to send this to in repsonse to the note which I just received
but perhaps you can pass the following statement along to whomever is
interested in this question of banning DIFABS. I wrote the following statement
as a frequent reviewer of ACS journals when I noted that DIFABS was routinely
being misused by more chemically-oriented authors. As a result of including
this statement with many rejected manuscripts, I have found that the editors of
several major ACS journals (apparently) no longer require my services. I
understand that they are concerned that a great deal of good chemistry is being
held up because of "less-than-perfect" crystal structures. I have much to say
about that subject too but I'll save that for later. Needless to say, if I had
know earlier that the journals would stop sending me manuscripts because my
ethical standards were too high, I would have written this statement much
sooner than I did!
SYSTEMATIC ERRORS
POLICY ON THE USE OF DIFABS AND SIMILAR PROGRAMS
TO ARTIFICALLY CORRECT THE OBSERVED DATA
FOR SYSTEMATIC ERRORS SUCH AS ABSORPTION
Systematic errors in x-ray diffraction data are virtually unavoidable.
Absorption effects are probably the best recognized source of systematic errors
and the ones which have received the most attention, at least in terms of the
number of programs which are available to 'correct' for these errors.
Extinction effects are generally a minor source of errors for organic and
organometallic compounds, but can be a significant source for inorganic
structures. But again, it is a source that almost everyone who has been in
business for some time recognizes and can deal with.
There are, however, other sources of systematic errors which can
potentially produce effects far more serious than those from absorption but
which are generally ignored or improperly corrected for, not that I am
particularly happy with all of the present algorithms for absorption
corrections. Sources included in this category are, for example, poor
diffractometer alignment, poor crystal alignment, the non-uniformity of the
x-ray beam on all diffractometers with incident-beam monochromators, and
decomposition effects. I have been amazed to find many institutions where
routine alignments are never done, or even if they are done, they are completed
only with the package of programs available from the manufacturer. Once the
computerized instrument alignment is done, very few people check to see that
the beam is actually centered on the crystal; on most instruments that I have
checked, the beam shines on only part of the crystal and the relative positions
of the tube tower, beam collimator, and the circle must all be adjusted. This
is made additionally critical because the beam from an instrument with an
incident-beam monochromator is non-uniform, generally taking on a pencil shape
(with either a vertical or horizontal sense depending on the monochromator
orientation) with a uniform beam width of no more than 0.2-0.3 mm. Thus, if a
diffractometer is not aligned properly, a major portion of the beam may be just
catching an edge of the crystal in one orientation, but only a corner in
another. Huge systematic errors may result. Even if the diffractometer is
aligned, improper optical alignment of the sample crystal can
also lead to serious errors; improper alignment may easily result, for example,
if the scope is knocked out of its proper position. Crystals larger than the
uniform beam size are also a source of errors. Decomposition effects too are
seriously under-estimated by monitoring low-angle 'standard reflections';
experiments show that, on average, a fifty percent drop in high-angle
intensities (MoKa, 2t = 50 deg) is accompanied by only a 10% drop in the type of
low-angle reflections that are normally used for standards (2t = 10-20 deg).
Furthermore, there are wide variations in the effects on individual reflections
within any 2t shell such that no correction is ever possible or appropriate!
Programs such as DIFABS have been developed to artificially correct for
all systematic errors in the data no matter what their source. Before its
development, systematic errors in the intensity data were 'refined' into the
anisotropic thermal parameters, and sometimes were so severe that all of the
atoms in a molecule would have nearly uniform ellipses elongated in the same
direction. Systematic errors were thus sometimes easily recognized by the
crystallographer, or failing that, by the reviewers. DIFABS, which attempts to
systematically correct all of the 'observed' intensities to better fit the
calculated intensities, is an ingenious program to help determine the presence
of systematic errors, but is being seriously, and increasingly misused as an
'absorption' correction program. The immediate effect of its use is that poor
data, full of various systematic errors, can be made over to look like perfectly
reasonable data. Its use in this manner represents a type of scientific fraud
in which the 'observed' data is modified to agree with a proposed model,
potentially hiding a number of serious systematic errors from reviewers,
journal readers and database personnel. The program has become the lazy man's
panecea for dealing with systematic errors; there is no need to deal with the
root causes of the systematic errors or, in the case of absorption, to attempt
a more appropriate correction. For these reasons, I will no longer accept
manuscripts for publication in which DIFABS has been used in this manner
because I have no real way of evaluating its effects on the data.
My experience with DIFABS, which in fact is quite extensive, has shown
that it not only corrects for the systematic errors noted above but also
'corrects' for the anisotropic motion of the heaviest atoms in the structure.
If there is only one heavy, it becomes spherical in shape; the light atom
ellipsoids are also distorted in the sense that the heavy atom motion is
'subtracted' from each of them. Thus, for the case of a single heavy atom,
all of the thermal parameters are distorted. Because DIFABS also allows for a
'2-theta' correction, even the absolute values of the thermal parameters may be
affected. With multiple heavy atoms, for example a polytungstate, the effects
on the thermal parameters are much less dramatic since the heavy atoms are
likely to have very different thermal motions to start with. As might be
expected from published surveys of multiple intensity-data sets, refinements
with and without the application of DIFABS show little change in bond distances
and angles when applied to reasonably good data sets. I (or anyone else that I
know of) have not made a systematic study of its effect on the refinements of
poor data sets with large built-in systematic errors.
DIFABS is a fantastic program when used as a diagnostic tool and,
as such, should be a part of every crystallographers bag of tricks. Its use
as a routine quick fix for poor intensity data cannot, however, be
scientifically justified.
Richard Harlow
harlow@esvax.dnet.dupont.com
From: huffman@indiana.edu (John C. Huffman)
Newsgroups: sci.techniques.xtallography
Subject: Re: DIFABS - SHOULD IT BE BANNED ??
Organization: Indiana University
Date: Tue, 26 Apr 1994 00:56:12 GMT
Several interesting and valid points have been made concerning the
absorption problem. As stated by Ton, one option is to require that
only "publication quality crystals" be submitted--but I doubt that
one would make many freinds doing this. We too have problems with
the shape of a crystal, expecially when we have one that is quite air
sensitive, etc., and we end up with a terribly irregular cyrstal in
a glob of grease. One possibility I have toyed with is to come up
with some amorphous material of approximately the same absorption
coefficient as the crystal in question and shape a sphere around the
sample. Presumably one could then use a spherical correction? Let's
face it, one normally ignores the fiber, the glue, and miscellaneous
other garbage that presumably one should worry about. Lucky for us
the problem is overdetermined by a factor of 5:1 to 15:1 and most
errors are averaged out to a large extent.
With the above in mind I can state that I always TRY to use the
indexed faces for the corrections. To verify the proper indexing,
and to locate any gross errors, we have a program that is used to
generate the absorption correction program input, and will draw the
crystal as mounted on the glass fiber. We can thus input the faces
and distances, the diameter of the fiber, and, using a cheap
graphics program have a rotating image of the mounted crystal
to compare with the one in the microscope. Believe me, this has
saved me on several occasions. Once satisfied with the comparison of
the real and generated crystal, the absorption correction input is
saved for later use. In conjuction with this, I have mounted video
cameras on the goniostat's microscope and recorded the images of the
crystal. By generating a hard copy of the calculated crystal
drawing one can adjust the size to see how well the two match. I
hope to be able to include images of the crystals as part of the
permanent "raw data" file by the end of this year. The cameras
themselves are quite cheap (under $500 for one with an interface
card to an IBM PC). In addition to having a permanent record,
one has a series of images which can be used to carefully measure
the crystal (I use a 1/64" steel ball image as the standard). How
do others obtain accurate measurements?
=============================================
John C. Huffman Senior Scientist
Indiana University Molecular Structure Center
Bloomington, IN 47408-4001 USA
---------------------------------------------
huffman@indiana.edu (812) 855-6742
=============================================
Newsgroups: sci.techniques.xtallography
From: alinden@oci.unizh.ch (Dr. Tony Linden)
Subject: Re: DIFABS - SHOULD IT BE BANNED ??
Organization: University of Zurich
Date: Tue, 26 Apr 1994 08:53:14 GMT
Ton Spek and his respondents raise some interesting points about DIFABS.
Perhaps we need an IUCr official recommendation on the use of this
procedure. Unfortunately, I suspect that this Newsgroup medium is not read
by sufficient crystallographers (yet) to canvas a good spectum of opinion.
Having read some of the responses, I will throw in my, perhaps naive,
comments.
Firstly, it would be interesting to hear the opinions of the creators of
DIFABS, Walker & Stuart in light of the 11 years of experience with their
procedure. I do not know of any comments they have made since the
publication of their paper. If anyone does know of such comments, I would
be pleased to hear them.
Surely when any type of absorption correction is applied, the primary data
is altered in such a way that the original raw data cannot be recovered from
deposited material. For example, psi scans are usually applied to Fo (or
Fo2) during data reduction. Therefore DIFABS is not the only culprit here.
Perhaps we need to deposit data containing Fo, Fo(corr) and Fc in the CIF
files (as suggested by Bill Harrison). In any event, if laboratories
archive their own data properly, the original uncorrected data should
always be available from the authors.
Any systematic errors that are of a spherical nature and equally affect all
reflections (perhaps there are none of this type) will not be noticed by
DIFABS. Also, when DIFABS calculates its absorption profile, the weak
reflections and any reflections where Fo and Fc are grossly different are
ignored, so that those reflections that contain the greatest systematic, or
extinction errors are not influencing the DIFABS correction. Admittedly
weaker extinction effects may be mopped up by DIFABS. As Ton Spek points
out, psi scans are not infallible if one of the scans happens to hit a
reflection suffering from extinction.
Systematic errors often show up in the Goodness-of-fit indicator at the end
of the refinement. A misaligned monochromator crystal (the crystal, not
the angle) resulted consistently in GoF values in the range 2.0-3.0,
although the R-factors were good. DIFABS did not help to reduce GoF by
polishing out the systematic error (ie DIFABS does not hide as much as some
might think). After the monochromator was correctly set, GoF was found to
be in the range 1.0-1.5 for most structures.
It actually takes more refinement time to do a DIFABS correction, if it is
done properly, although time spent at the diffractometer is obviously less
if crystal or psi scan measurements are not done.
People seem concerned that DIFABS may improve R too drastically (examples
given were from 0.08 to 0.05 or from 0.15 to 0.05). While this may give an
uneasy feel, we really should compare the improvement in R made on the same
structures by other correction methods before discarding such changes as
inappropriate. I have seen the R for heavy atom structures undergo similar
changes with a numerical correction.
I see that Acta Cryst now frowns upon "Transmission coefficients" greater
than 1.1. This is awkward, since DIFABS normalises the correction
coefficients (not really a transmission coeff, but the effect is the same)
to give a mean of approx 1.0 and Tmax of 1.2 is not uncommon.
Some obviously feel that the thermal parameters are "rounded" or even
meaningless after a DIFABS correction. Maybe so, although I have
experienced cases where the thermal ellipsoids expanded (ever so slightly)
as a result of the correction, so nothing was being "hidden".
One of the biggest dangers for the misuse of DIFABS is applying it
inappropriately, or at the wrong stage of the refinement, and this is
possibly where the ill-informed worker has fallen into the trap. Since the
correction relies on the adequacy of the structural model, it is imperative
that the model be as near to correct as possible. This includes having as
many of the H-atoms in the model as possible, as well as having any
disorder (most important!) sorted out BEFORE the correction is applied.
Additionally the correction should be applied to the model with isotropic
temperature factors, since after an anisotropic refinement, the thermal
parameters will mop up some of the effects of absorption. This does not
mean, of course that an anisotropic refinement cannot already have been
done, as an aid to finding H-atoms, for example, but the model should be
converted back to isotropic before the correction.
The above comments on aniso thermal parameters raises another interesting
question. Are the thermal parameters after the DIFABS correction really
meaningless, as suggested by Nat Alcock, or is the uncorrected data
producing meaningless thermal parameters, because of the (ignored) effects
of absorption being mopped up in the guise of thermal motion?
I believe that DIFABS has its place if used appropriately. The difficulty
is to educate people, especially the casual non-crystallographer who has a
diffractometer in his/her lab as a purely analytical tool, as to when and
when not to employ such a procedure. DIFABS should not be used ad hoc, but
only when the crystal morphology and mu warrant an absorption correction.
For example, people should not blindly accept a large correction for a nice
isotropic organic crystal. Further, if the opportunity exists to collect
psi scans, this should be done. Both Enraf-Nonius and Rigaku/MSC systems
(at least) have this option automated into their data collection programs.
Indexing the faces of the crystal is also recommended (perhaps the best
procedure), but the problem often occurs that the crystal is ill-faceted,
or sealed in a capilliary with a liquid, which makes such measurements
impractical - we do not always get perfectly formed crystals delivered to
us, do we?
Unusual features in structures are often queried if DIFABS has been
employed. In my experience, the unusual feature was not modified in any
way by employing uncorrected reflection data, so I do not believe that
DIFABS is capable of introducing significant "new features" or wiping out
undesirable ones, PROVIDED the program is used properly (see above). Here,
I am willing to accept evidence to the contrary.
A final question for thought and comment. In cases where an absorption
correction is definitely warranted and psi scans or numerical methods are
not practical, what is the best approach?
- Apply no correction and have the refined model (and conclusions drawn
therefrom) biased by errors in the intensities. This is the route
apparently advocated by some respondents.
- 2. Attempt to correct the errors in the intensities, at least to some
extent, and perhaps in doing so decrease the bias on the model (although
the originally biased model may to some extent bias the corrections - a
vicious circle? I suspect, however, the correction would at least push the
bias towards the true model). As long as the souce of the correction is
stated, you are not hiding anything and a reader should be able to draw
his/her own conclusions.
I am willing to be shot down in flames for my opinions (I am always ready
to learn), but at least I hope this will enliven the discussion...
I think that the end result of this discussion will show that some of us
need to get together to undertake a systematic study of the effects on all
aspects of a structure of the various correction methods, for both weakly
and strongly absorbing materials.
Tony.
Dr. Anthony Linden Tel: +41 1 257 4228
Organic Chemistry Institute Fax: +41 1 361 9895
University of Zurich E-mail: alinden@oci.unizh.ch
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
From: dewar@cs.nyu.edu (Robert Dewar)
Newsgroups: sci.techniques.xtallography
Subject: Re: DIFABS - SHOULD IT BE BANNED ??
Date: 26 Apr 1994 10:03:35 -0400
Organization: Courant Institute of Mathematical Sciences
Reading the discussion on DIFABS, it seems hard to escape the obvious
conclusion, which is that full disclosure is required. As long as people
know that DIFABS has been used, then they can apply their own valud
judgments to the resulting data. Cearly it would be valuable to deposit
both the original (true or messy, depending on your point of view) data
and the DIFABS'ed data (cleaned up or faked, depending on your point of
view).
(incidentally, I find it entertaining that Internet allows me to follow
what's going on in the field a little bit these days. THe last work I
did in crystallography was my Phd thesis work (early automation of direct
methods using the programs MAGIC and MAGIA), and it is interesting to see
how far the field has come in making the transition from structure
determination being quite a challenge to being quite routine at least in
simple cases :-)
Robert Dewer
Newsgroups: sci.techniques.xtallography
From: jvs@helix.nih.gov ("Jim Silverton")
Subject: DIFABS
Date: Thu, 28 Apr 94 09:28:35 EDT
Organization: NIH
Given the misgivings expressed by several people concerning the deposition
of massaged as opposed to raw data, perhaps it is time for journals like
Acta to consider asking for the diffractometer output. An initial reaction
might be that the volume of data would get out of hand but the sizes of
such files are not as large as one might initially guess. It would not be
all that much trouble to set up an FTP server for access over the Internet.
After all, the ACS already has one.
To illustrate file sizes, the CAD4.DAT file for a steroid occupied 40 960
bytes. When compressed with gzip the file size was 11 238. Neither would
take very long to access and the zipped file is really very small.
Changing the subject! Crystallographers might like to get the low down on
themselves by reading a new "non-fiction" book: "The Billion Dollar
Molecule" by Barry Worth, Simon and Schuster, 1994, ISBN: 0671723278. I
will leave the value as an exercise to the reader!
James V. Silverton
NIH, Bldg. 10, Room 7N-309, Bethesda MD 20892, USA.
Phone:301.496.1515 Fax:301.402.3404
Newsgroups: sci.techniques.xtallography
From: flack@scsun.unige.ch (FLACK Howard)
Subject: Re: DIFABS
Organization: University of Geneva, Switzerland
Date: Thu, 28 Apr 1994 15:12:49 GMT
In article jvs@helix.nih.gov ("Jim Silverton") writes:
> Given the misgivings expressed by several people concerning the deposition
> of massaged as opposed to raw data, perhaps it is time for journals like
> Acta to consider asking for the diffractometer output.
No, Jim, not the native diffractometer output files which often do not contain much
of the information that one wants to save and are often in binary with undocumented
fields. I suggest the following:
As a by product of a collaboration with people down the road where we had to
exchange raw data files coming from different machines, we produced a FORTRAN
programme that lets you put the raw data into a standardized form e.g. CIF. Here's
some of my blurb about DIFRAC
(marked up in HTML) taken from the file on the
"Crystallography in Europe" World Wide Web server on URL:
http://www.iucr.org/cww-top/crystal.index.html
(Old address was: http://www.unige.ch/crystal/crystal_index.html)
You can get the programme from me free by e-mail. When I have 5 spare seconds one
day, I'll set it up on an anonymous ftp server.
DIFRAC
blurb
DIFRAC
converts single-crystal diffractometer output
files as produced by manufacturers' software into a standardized instrument-
independent form consisting of a clear, complete, well-documented record of the
sample and the diffraction measurements performed upon it. Information not
already available in the manufacturers' diffractometer files is obtained in an
interactive question-and-answer session. The software is written in a modular
way. Available modules can treat Enraf-Nonius CAD-4, Philips PW1100,
Siemens P21 and Stoe DIF4 single-crystal diffractometers, and
produce output in CIF (Crystallographic Information File) or
SCFS (Standard Crystallographic File Structure) format.
Reference: 'DIFRAC,
single-crystal diffractometer output-conversion
software' by H.D. Flack, E. Blanc and D. Schwarzenbach (1992),
J. Appl. Cryst.25, 455-459.
DIFRAC
is distributed by e-mail. Contact flack@scsun.unige.ch for a copy.
H.D.F.
H. D. Flack
Laboratoire de Cristallographie ! Telephone [+[41] 22] 702 62 49
University of Geneva ! Telefax [+[41] 22] 781 21 92
24 quai Ernest-Ansermet ! Telex ch-42 11 59 siad
CH-1211 Geneve 4 ! e-mail(rfc-822) flack@scsun.unige.ch
Switzerland !
Newsgroups: sci.techniques.xtallography
From: jvs@helix.nih.gov ("Jim Silverton")
Subject: DIFABS (revision of message re. FTP and deposition of files)
Date: Thu, 28 Apr 94 11:31:51 EDT
Organisation: NIH
Sorry everyone!
Because of a transmission fault the file sizes given in the previous
version of this post are quite incorrect. The transmission between the VAX
and the UNIX machine failed but I did not get an error message thus the
data file was somewhat smaller than reality. I don't think the emphasis is
changed by the correct figures and I will post the rest of the message as
before. The only changes are the file sizes
Given the misgivings expressed by several people concerning the deposition
of massaged as opposed to raw data, perhaps it is time for journals like
Acta to consider asking for the diffractometer output. An initial reaction
might be that the volume of data would get out of hand but the sizes of
such files are not as large as one might initially guess. It would not be
all that much trouble to set up an FTP server for access over the Internet.
After all, the ACS already has one.
To illustrate file sizes, the CAD4.DAT file for a steroid occupied 289408
bytes. When compressed with gzip the file size was 79839 bytes. Neither
would take very long to access and the zipped file is really quite small.
Changing the subject! Crystallographers might like to get the low down on
themselves by reading a new "non-fiction" book: "The Billion Dollar
Molecule" by Barry Worth, Simon and Schuster, 1994, ISBN: 0671723278. I
will leave the value as an exercise to the reader!
James V. Silverton
NIH, Bldg. 10, Room 7N-309, Bethesda MD 20892, USA.
Phone:301.496.1515 Fax:301.402.3404
From: dewar@cs.nyu.edu (Robert Dewar)
Newsgroups: sci.techniques.xtallography
Subject: Re: DIFABS (revision of message re. FTP and deposition of files)
Date: 29 Apr 1994 10:39:37 -0400
Organization: Courant Institute of Mathematical Sciences
To put some perspective on file sizes and costs, the cost of sufficient
disk space to accomodate the compressed raw CAD4.DAT file is about $0.02
just my two cents :-)
Newsgroups: sci.techniques.xtallography
From: jvs@helix.nih.gov ("Jim Silverton")
Subject: Difabs and absorption corrections
Date: Mon, 2 May 94 10:22:19 EDT
Organistations: NIH
A major problem with analytical absorption corrections is the horrible real
facts of life. I often have to carve out an irregular chunk and sometimes
also have to seal it up with solvent etc. I would like to grind a sphere
but many organic crystals disintegrate completely when I try. I have done a
recent count and have found that only one of the last six crystals I have
looked at could be said to have a shape accurately describable by crystal
faces. Maybe a photographic technique could be developed but I suspect Psi
scans will remain popular.
The mathematical or tabular form of an empirical absorption correction like
a psi-scan is quite simple and should be deposited in conjunction with
structure factor tables, especially if the journals won't take raw data or
some modification as suggested by Howard Flack. Incidentally, if Howard's
program or something like it were to be required, I think it should be the
journal's responsibility to make the program readily and continuously
accessible (in other words FTP). However, I would really prefer an ASCII
file compressed by some GENERIC program like gzip.
James V. Silverton
NIH, Bldg. 10, Room 7N-309, Bethesda MD 20892, USA.
Phone:301.496.1515 Fax:301.402.3404
Newsgroups: sci.techniques.xtallography
From: flack@scsun.unige.ch (FLACK Howard)
Subject: Re: Difabs and DIFRAC
Organization: University of Geneva, Switzerland
Date: Tue, 3 May 1994 16:54:37 GMT
In article jvs@helix.nih.gov, jvs@helix.nih.gov ("Jim Silverton") writes:
> Incidentally, if Howard's
> program or something like it were to be required, I think it should be the
> journal's responsibility to make the program readily and continuously
> accessible (in other words FTP).
OK the penny has dropped. DIFRAC
is now available by anonymous ftp from our site
since I can not imagine a journal providing a service like that. The "instructions"
are given below. I did not gzip the files since the programme is supposed to run
on all sorts of platforms and the compression programmes seem to be rather system
dependent. (But may be you could convince me otherwise). Whats available are ASCII
source code files and documentation.
I also put the necessary hypertext links for DIFRAC
into the appropriate place in the "Crystallography in Europe" WWW server on URL:
http://www.iucr.org/cww-top/crystal.index.html
which is much less cumbersome to use than direct anonymous ftp
README.1ST
DIFRAC
Single-Crystal Diffractometer Output-Conversion Software
By H.D. Flack, E. Blanc and D. Schwarzenbach
Contact: H.D. Flack E-mail: flack@scsun.unige.ch
Reference: J. Appl. Cryst. (1992) 25, 455-459
Distribution: By anonymous ftp
from: ftp://ftp.unige.ch/pub/soft/crystal/difrac/
The description material is in the file [ancill.mat]. Recover this file
first and read the text to find out which files you need for your
application.
All files are ASCII and unpacked.
Newsgroups: sci.techniques.xtallography
From: huffman@indiana.edu (John C. Huffman)
Subject: Re: Was DIFABS (hand laser alignment of single xtal diffractometers)
Organization: Indiana University
Date: Tue, 3 May 1994 20:40:34 GMT
In article <199405010918.AA01427@sol.dmp.csiro.au>, lachlan@dmp.csiro.au (Lachlan Cranswick) writes:
|>
|> [stuff deleted]
|>
|> I'm not sure if this type of thing is old news to people but
|> the research XRD lab next door recently had alignment
|> problems with an re-hashed Siemens AED
|> 3 circle diffractometer. They used a A$100 pencil laser normally
|> applied to lectures and seminars to realign the diffractometer
|> while it was potentially in a horrible state.
|>
|> While this diffractometer was/is regularly aligned, during a trip
|> home from having a modern tube tower installed,
|> the tube tower base suffered some
|> structural damage. This threw the factory alignment settings out
|> and was potentially a major job to realign (the factory
|> alignment tools were not available).
|>
|> Instead a pencil laser was purchased that made the alignment
|> very easy :-
|>
|> The tube tower was moved out of the way.
|>
|> The laser was mounted on a retort stand.
|>
|> [more deleted]
|>
|> Lachlan Cranswick - CSIRO
I think the use of lasers is not routine simply because there is not
enough of a market to entice one of the instsrument makers into making
a good laser alignment tool. Because I have quite a few Pickers to
align (I believe in periodic checks also!) I had two rather simple-
minded laser alignment devices made some time ago. One is attached to
the top of what was an X-ray tube and is fixed with a 45 deg mirror
so that one can place the laser assembly in the tube housing as though
it were an X-ray tube (of course you can't adjust the take-off angle).
A second laser is affixed to the track that the scintillation counter
fits on on the goniostat. The latter can be used without messing
around with the tube. A small (5 mm) front surface mirror mounted
on a gnoiometer head, as well as a 1/64" sphere are used in various
ways to check the beam path. Believe me, I feel much safer when
I do the alignment using this system!
Another trick I use on the Picker systems is a specially built "surface
plate" that can be used in conjunction with precision machinist dial
indicators and height guages to assist in the preliminary alignment.
I have had several specialized alignment tools constructed over the
years which make it easy to perform the crude alignment.
For the final alignment we use BeOAc crystals and ruby spheres. We have
installed a command for the goniostat which will measure a given
reflection in the eight accessible locations and tell the user what
adjustments need to be made (see the International Tables--I think they
give the formulas?).
In any case, I certainly agree that careful absorption corrections
are meaninless if you don't have a grasp on the other errors that
are present. Carefully measuring and indexing the faces does no
good if the crystal is not fully bathed in a uniform beam.
=============================================
John C. Huffman Senior Scientist
Indiana University Molecular Structure Center
Bloomington, IN 47408-4001 USA
---------------------------------------------
huffman@indiana.edu (812) 855-6742
=============================================
Newsgroups: sci.techniques.xtallography
From: lachlan@dmp.csiro.au (Lachlan Cranswick)
Subject: TENTATIVE "BANNING OF DIFABS" SUMMARY?
Organization: CSIRO Division of Mineral Products, Melbourne, AUSTRALIA
Date: Wed, 8 Jun 1994 02:30:52 GMT
Hi All,
Recently there are was a discussion about the "BANNING OF DIFABS"
This was a most un-Usenet like discussion. Instead of people using
the time to insult and "flame" eachother, the discussion "seemed" to
arrive at compatable conclusions.
There was a comment during the DIFABS discussion that this "Newsgroup
is not read by sufficient crystallographers (yet) to canvas a good
spectum of opinion". Thus, would participants and readers be
interested in generating a summary for submition to a conventional
paper journal (recommendations?). This would help assist in the
wider propogation of the concerns and conclusions.
It would also be nice to think that discussions like this could
become routine in the not to distant future.
Tentative Summary of DIFABS Discussion.
Do people think the following is a fair summary of the discussion or
are there things to add or delete? This is a mish-mash of comments
and statements made by participants and no doubt could be put in
better categories and priorities.
There is concern over the use and misuse of absorption
correction software such as DIFABS to determine crystal structures.
Via discussion, this has resulted in the following actions and
conclusions? :-
- Raw data (not just corrected) should be provided with the
abstract in CIF format. The size of raw data files is not an
archiving problem given the size of modern tape and hard-disks.
- The DIFRAC
software by Flack and Schwarzenbach for
converting binary diffractometer data from several commercial
diffractometers into CIF (or SCFS) format is available via anonymous
FTP at
ftp://ftp.unige.ch/pub/soft/difrac
(J. Appl. Cryst. (1992) 25, 455-
459). Thus there is now no excuse for raw (CIF) data not to be
submitted to the journal.
- More emphasis, if possible, on "customers" providing journal
quality crystals for analysis.
- Psi-scans (when possible?) be encouraged and performed.
- Time effective, accurate face-indexed measurements of the
crystal can be done off the diffractometer and should be encouraged.
- DIFABS (and similiar software) is a legitimate(?) package
in the crystallographer's "back of tricks" - but users should
be made aware of its abuses and effects (e.g. software correction for
poorly installed and aligned equipment, inappropriate stages of the
refinement to be using the correction software).
- Use of such correction software should be explicitly stated
with "real" Fo and "corrected" Fo submitted.
- There is no justification for publishing thermal ellipsoid
diagrams after DIFABS has been used.
- Methods for the easy, safe checking and alignment of single
crystal diffractometers are available and possible with even home
made equipment. For instance, using equipment such as cheap hand
lasers, it is potentally a trivial and safe job to check that the
X-ray beam is bathing the entire crystal. Routine checking of
equipment should be encouraged to minimize the abuse of absorption
correction software to correct for systematic errors caused by poor
alignment and/or partial irradiation of the crystal.
- Relatively cheap methods exist for obtaining computer (or
visual) images of the crystal on the goniometer for comparison with
computer generated drawings of the crystal.
- A "round robin" comparing the effects of "various?"
absorption correction software vs uncorrected results would be
beneficial.
One of the results from the IUCr CPD Rietveld Refinement Round
Robin I, - (R.J. Hill, J Appl. Cryst. (1992) 25, 589-610) follows
which is semi relevant :-
"It is appropriate to mention here that an error was discovered
in the DBW3.2S code during in-house analysis of the m-ZrO2 data
submitted during the course of Part II of the project. This error
involved an incorrect assignment of the multiplicity of reflections
of the type 0kl in the point group 2/m. Although not producing
a catastropic refinement result, the profile agreement indices were
larger than normal and the derived crystal structure parameters
showed a wider than expected deviation from the accepted values.
All participants who used this software wre informed of a cure
to the problem and asked to submit a reanalysis of their
m-ZrO2 data. This is a clear example of the important role
that intercomparison projects can have in highlighting problems
with refinement software."
Lachlan.
Lachlan Cranswick - CSIRO _--_|\ lachlan@dmp.CSIRO.AU
Division of Mineral Products / \ tel +61 3 647 0367
PO Box 124, Port Melbourne \_.--._/ fax +61 3 646 3223
3207 AUSTRALIA v
From: sp@oedipus.llnl.gov
Newsgroups: sci.techniques.xtallography
Subject: Re: TENTATIVE "BANNING OF DIFABS" SUMMARY?
Date: Thu, 09 Jun 94 11:14:41 PDT
Organization: Lawrence Livermore National Laboratory, NCD
In article <1994Jun8.023052.17411@dmp.csiro.au>, writes:
A few thoughts in response to Lachlan's note:
> - More emphasis, if possible, on "customers" providing journal
> quality crystals for analysis.
If the only crystals to ever see a diffractometer were of good quality,
current chemistry would be at the state it was at about 30 years ago and
structural biology as a science would be non-existent. It would be more
appropriate to emphasize the fact that data-collection strategies can be
altered to accomodate the crystal at hand. See Hope, H. 'Progress in
Inorganic Chemistry' vol. 41 pp 1-19.
> - Time effective, accurate face-indexed measurements of the
> crystal can be done off the diffractometer and should be encouraged.
In the few cases that crystals have nice faces.
> - DIFABS (and similiar software) is a legitimate(?) package
> in the crystallographer's "back of tricks" - but users should
> be made aware of its abuses and effects (e.g. software correction for
> poorly installed and aligned equipment, inappropriate stages of the
> refinement to be using the correction software).
Diffractometer misalignment is lamentable, but it is not a function of
the absorption correction routine used. Banning of DIFABS etc. is not
an appropriate response to poorly maintained equipment.
> - Use of such correction software should be explicitly stated
> with "real" Fo and "corrected" Fo submitted.
I agree. However, since absorption, extinction, TDS etc. are real
physical phenomena, wouldn't it be better to account for them in Fc or
Fc^2 ?
> - There is no justification for publishing thermal ellipsoid
> diagrams after DIFABS has been used.
This response seems to be the result of emotion. A satisfactory
conclusion would come from a comparison of thermal parameters obtained
after DIFABS (or XABS2) and after a rigorous face-indexed correction.
It is likely that in many cases, that empirically corrected data will
produce thermal ellipsoids that are closer to reality than uncorrected
data. Does that mean that thermal ellipsoid plots for structures with
no absorption correction should be (uncritically) banned ?
> - Methods for the easy, safe checking ...
Anything that stresses increased respect for the experiment is to be
encouraged. There is still no correlation between it and absorption
correction algorithms.
Sean Parkin
sp@oedipus.llnl.gov
From: msrbb@csv.warwick.ac.uk (N W Alcock)
Newsgroups: sci.techniques.xtallography
Subject: Re: TENTATIVE "BANNING OF DIFABS" SUMMARY?
Date: 10 Jun 1994 12:55:16 +0100
Organization: University of Warwick, Coventry, UK
In article <2t7p5f$g6h@lll-winken.llnl.gov>,
sp@oedipus.llnl.gov writes:
> Lachlan Cranswick writes:
>> - There is no justification for publishing thermal ellipsoid
>> diagrams after DIFABS has been used.
>
>This response seems to be the result of emotion. A satisfactory
>conclusion would come from a comparison of thermal parameters obtained
>after DIFABS (or XABS2) and after a rigorous face-indexed correction.
>It is likely that in many cases, that empirically corrected data will
>produce thermal ellipsoids that are closer to reality than uncorrected
>data. Does that mean that thermal ellipsoid plots for structures with
>no absorption correction should be (uncritically) banned ?
>
Seeing that DIFABS works by setting the mean values of the anisotropic
displacement parameters to be equal, it follows that ANY systematic
variation in anisotropy will be eliminated by its use. One can clearly see
in published papers that anisotropic plots for over-DIFABS-corrected
structures show notably round atoms. Neglect of a proper absorption
correction where the problem is moderate (say Tmin = 0.8; with 10%
variation in T) should not have a disastrous effect on the thermal parameters.
If severe absorption is neglected, especially if highly anisotropic, the
thermal parameters will undoubtedly be meaningless - but the structure should
probably not be published in that state at all!
> The small proportion of crystals with measurable faces
One can only use personal experience to judge how big a problem this really
is. Of the crystals we see in our lab, I would estimate that at least 85%
have well defined and measurable faces. In my view, the comment is not
justified.
Nat Alcock, University of Warwick
msrbb@snow.csv.warwick.ac.uk
Newsgroups: sci.techniques.xtallography
From: flack@scsun.unige.ch (FLACK Howard)
Subject: Re: TENTATIVE "BANNING OF DIFABS" SUMMARY?
Sender: usenet@news.unige.ch
Organization: University of Geneva, Switzerland
Date: Fri, 10 Jun 1994 13:33:37 GMT
In article 17411@dmp.csiro.au, lachlan@dmp.csiro.au (Lachlan Cranswick) writes:
> - The DIFRAC
software by Flack and Schwarzenbach for
should read
by Flack, Blanc and Schwarzenbach for
> converting binary diffractometer data from several commercial
should read
converting (possibly binary) diffractometer data .......
H.
From: sp@oedipus.llnl.gov
Newsgroups: sci.techniques.xtallography
Subject: Re: TENTATIVE "BANNING OF DIFABS" SUMMARY?
Date: 10 Jun 94 16:13:26 GMT
Organization: Lawrence Livermore National Laboratory, NCD
I wrote:
> > The small proportion of crystals with measurable faces
In article <2t9kb4$5lb@crocus.csv.warwick.ac.uk>,
writes:
> One can only use personal experience to judge how big a problem this really
> is. Of the crystals we see in our lab, I would estimate that at least 85%
> have well defined and measurable faces. In my view, the comment is not
> justified.
In the last 3 years, I have had direct experience with well over 100 small
molecule crystal structures. Exactly one (1) of which had measurable faces.
Absorption correction for this crystal was of the rigorous face indexed type.
Sean Parkin
sp@oedipus.llnl.gov
Newsgroups: sci.techniques.xtallography
From: lachlan@dmp.csiro.au (Lachlan Cranswick)
Subject: 2ND TENTATIVE DIFABS SUMMARY
Organization: CSIRO Division of Mineral Products, Melbourne, AUSTRALIA
Date: Fri, 1 Jul 1994 14:10:40 GMT
2ND TENTATIVE DIFABS SUMMARY
A discussion on whether the absorption correction software, DIFABS,
should be banned, was started on April 20th by Tom Spek and seems
to have reached compatable conclusions.
It is hoped a agreed summary can be generated and submitted
to an appropriate journal.
The aims of a journal article would be to raise awareness
of both the potential applications of this newsgroup, and
the DIFABS issue.
There is concern over the use and misuse of absorption
correction software such as DIFABS to determine crystal structures.
Via discussion, this has resulted in the following actions and
conclusions :-
- DIFABS (and similiar software) is a legitimate package
in the crystallographer's "back of tricks" - but users should
be made aware of its abuses and effects (e.g. software correction for
poorly installed and aligned equipment, inappropriate stages of the
refinement to be using the correction software).
- Raw data (not just corrected) should be provided with the
abstract in CIF format. The size of raw data files is not an
archiving problem given the size of modern tape and hard-disks.
- The DIFRAC
software by Flack, Blanc and Schwarzenbach for
converting (possibly binary) diffractometer data from several commercial
diffractometers into CIF (or SCFS) format is available via anonymous
FTP at
ftp://ftp.unige.ch/pub/soft/difrac (J. Appl. Cryst. (1992) 25, 455-
459). Thus there is now no excuse for raw (CIF) data not to be
submitted to the journal.
- More emphasis, if possible, on "customers" providing journal
quality crystals for analysis.
Where this is not practical, data-collection strategies can be
altered to accomodate the crystal at hand. i.e.:-
- Psi-scans
- Time effective, accurate face-indexed measurements of the
crystal done off the diffractometer.
- Relatively cheap methods exist for obtaining computer (or
visual) images of the crystal on the goniometer for comparison with
computer generated drawings of the crystal.
- Other techniques [and order of preference?]
Use of such correction software should be explicitly stated
with the following submitted :-
[which are recommended - 1 or all?]
- "real" Fo and "corrected" Fo.
- Fc
- Fc^2
Methods for the easy, safe checking and alignment of single
crystal diffractometers are available and possible with even home
made equipment. For instance, using equipment such as cheap hand
lasers, it is potentally a trivial and safe job to check that the
X-ray beam is bathing the entire crystal. Routine checking of
equipment should be encouraged to minimize the collection of
poor quality data. Thus minimizing concerns about
the abuse of absorption correction software
to correct for systematic errors caused by poor
alignment and/or partial irradiation of the crystal.
A "round robin" comparing the effects of "various?"
absorption correction software vs uncorrected results would be
very beneficial.
Comments Please :-
Lachlan.
--
Lachlan Cranswick - CSIRO _--_|\ lachlan@dmp.CSIRO.AU
Division of Mineral Products / \ tel +61 3 647 0367
PO Box 124, Port Melbourne \_.--._/ fax +61 3 646 3223
3207 AUSTRALIA v
From: st22@cornell.edu (Steve Trail)
Newsgroups: sci.techniques.xtallography
Subject: DiFabs - where can I find it?
Date: Thu, 2 Feb 1995 20:02:32 UNDEFINED
Organization: Cornell University
Is DiFabs available to the general public? If so, where? Any comments on it?
Thanks in advance,
Steve
******************
Steven Scott Trail
Chemistry Department
Cornell University
st22@cornell.edu
******************
From: jbridson@kean.ucs.mun.ca John Bridson
Newsgroups: sci.techniques.xtallography
Subject: Re: DiFabs - where can I find it?
Date: 6 Feb 95 14:35:57 -0230
Organization: Memorial University. St.John's Nfld, Canada
Someone else has already responded with help on getting DiFabs - you also
asked for comments. There was an outbreak of grumbling and suspicion a
year or so ago - the results are sometimes a little too good to be true
perhaps ?? I have used it in difficult structures as a last resort - it
has sometimes permitted me to get disordered groups sorted out at the very
end of least-squares cycling so I guess it sometimes has a real effect on
fit. HOWEVER, for every occasion it has worked I can cite two or three
times when the results have been very dubious and I would prefer to use
other absorption corrections if at all possible, even if the R values
aren't quite as good. The bottom line I guess is use it with suspicion and
great caution !
From: lmh@celia.caltech.edu (Henling, Lawrence M.)
Newsgroups: sci.techniques.xtallography
Subject: Re: Absorption correction programs
Date: 22 Feb 1994 12:08 PDT
Organization: California Institute of Technology
In article <94052.111949RXB116@psuvm.psu.edu>, writes...
>I'm looking for a (FORTRAN) program that could help me correct my
>data for absorption effects. The data was obtained for a single
I have the following DIFABS program, but have never used it:
larry henling
lmh@shakes.caltech.edu
In the subsequent e-mail messages are files for running
DIFABS; including the source code of the latest version (V9.0)
which uses an improved model for the absorption surface. For
details, please read the comments at the beginning of the
program.
I have sent a short description of the files that are
required and how the Fo^2/Fc^2 file may be generated if using
the SHELXL93 refinement program. The roundabout procedure
previously required for SHELX-76 and SHELXTL-PLUS is no longer
required.
Although the routines for the calculation of spherical
polar angles are general for any four-circle diffractometer data
collection geometry, in some instances extra code may be
required in routine ANGLES for the calculation of Eulerian
angles from the orientation matrix and reflection indices.
Despite testing these routines as thoroughly as possible, I
should state that my personal experience is only with
Syntex P21, Siemens P4 and CAD4 in the bisecting position.
Therefore, I suggest that you check that the Eulerian angles
calculated by the program are consistent with those output by
your diffractometer, and that the calculated polar angles are
consistent with the direction senses given in Fig. 1 and
equations (A1) in the 1983 Acta Cryst. paper.
I believe that the program code conforms fully to the
Fortran-77 standard and that although developed on a VAX
computer does not contain any of the extra facilities provided
by VAX/VMS Fortran (except those calls highlighted at the
beginning of the program). The following files are being sent:
1) Fortran source of DIFABS V09.0 DIFABS93.FOR
2) Test input parameter file DIFABS.DAT
3) Test input Fo^2/Fc^2 data file SROAC.FCF
4) Test output corrected Fo^2 data file SROAC.ABS
5) VAX/VMS job-control command file DIFABS.COM
6) Output listing file DIFABS.LIS
7) Integration with SHELXL93 text SHELXL93.TXT
The test data set is that of SROAC with generated absorption
errors, as mentioned in the Acta Cryst. papers. For information
on when and how to use this method of absorption correction, I
refer you to the 1983 Acta Cryst. paper.
From: chkennard@uqvax.cc.uq.oz.au (Colin Kennard, University of Queensland)
Newsgroups: sci.techniques.xtallography
Subject: Re: Absorption correction programs - where do you get it
Date: 23 Feb 94 11:46:32 AEST
Organization: The University of Queensland
Sorry to be dumb but the files never arrived here at UQ, are they available
by FTP or could they be posted directly to me please
Thanks
Karl
**************************************************************************
Karl A. Byriel ,-_|\
Department of Chemistry, / \Brisbane
The University of Queensland \_,-._/
QLD. 4072 Australia. v
email: byriel@chem.chemistry.uq.oz.au IP : 130.102.84.15
phone: 61-7-365 4300 fax: 61-7-365 4299
***************************************************************************
From: lmh@celia.caltech.edu (Henling, Lawrence M.)
Newsgroups: sci.techniques.xtallography
Subject: Absorption corrections
Date: 23 Feb 1994 21:41 PDT
Organization: California Institute of Technology
[I sent copies of DIFABS to all who requested it; if not received
please send e-mail and I will try again.]
We do not use DIFABS here as some people don't like it.
Instead, we use either an analytical absorption calculation or
an empirical psi-scan correction.
The analytical absorption calculation is the Gaussian quadrature
method of Busing and Levy (Acta Crys, 10, 180, 1957). It involves
measuring the phi and chi angles and centroid-face distance for
all faces and then integrating over an 8x8x8 grid.
When the faces cannot be measured (eg, obscured by grease in a
capillary), we measure psi-scans for 6 reflections at 10 degree
intervals. The plotted relative intensities are used to generate
a correction curve based on phi which is then applied to the data.
The second method should not be as good as the first
(dependent on the crystal shape), yet we have found that
the psi-scan method is often slightly better, based on the
goodness of fit for merging symmetry-equivalent reflections.
It will be interesting to compare our calculations with those
of the program recently posted.
larry henling
lmh@shakes.caltech.edu
Where do you get the DIFABS and XABS2 software?
From: TWEAKLEY@OREGON.UOREGON.EDU(Timoth J R Weakley)
Newsgroups: sci.techniques.xtallography
Subject: DIFABS
Date: 8 May 1995 23:29:36 -0000
Organisation: U. of Oregon
I've only just read the feature article in the latest IUCr Bulletin
and learned
- (i) that the newsgroup exists and
- (ii) that there has been a discussion on the
validity of absorption corrections by DIFABS, a
program I use as part of the TEXSAN v.5.0 (1989) package and rely on.
I'd like to add my twopennyworth of comments for what they're worth,
particularly as Acta Cryst. seems to be rather hostile to DIFABS. By
the way, has Nigel Walker been asked for or offered comments?
I assume the crystal was centered, the cell was well determined,a full
set of independent reflections was collected, the scan speed was not
excessive, background intensities were properly measured, etc.; also,
that the spacegroup is correct, the atoms have been properly
identified by element, and so on. Then if the DIFABS calculation has
been run after isotropic refinement of the complete structure
(excluding H atoms) the following should in my experience be true.
- For fibre-mounted crystals, the range of `transmission factors'
output by DIFABS correlates well with the max. amd min. transmission
in a smoothed and averaged psi-scan curve based on several reflections.
- If mu for such a crystal is large, the application of DIFABS leads
to a substantion reduction in residuals and in sigmas of coordinates
and derived dimensions after further isotropic refinement, and gets
rid of a lot of (chemically) meaningless residual electron density
peaks near heavy atoms.
- For a fibre-mounted crystal of low mu, DIFABS does not lead to any
significant reduction in residuals, GOF, and sigmas.
- For a capillary-mounted crystal of moderate mu, DIFABS often leads
to substantial improvement as in 2, above? It seems to be compensating
for absorption/scattering by glass and grease, etc. All right, so the
"improvement" may be cosmetic; but in that case, why is it that the
post-DIFABS model always seems more acceptable on chemical grounds,
if the physics is so suspect?
Further comments.
- Psi-scans: sometimes there are no adequately strong reflections in
the chi range 80-100 deg.; if the crystal happens to have two short
axes roughly normal to the phi-axis, there may be no useable
reflections at all.
- Absorption corrections based on the measured distances of identified
bounding faces of the crystal from a common interior point:
- (i) For highly-absorbing thin plates or elongated needles, the
corrections are highly sensitive to errors in linear measurement, which
may worsen the data instead of improving it (them?). Have you tried
measuring a distance of 0.02 mm recently, even under a good
microscope?
- (ii) The available crystals may all be irregular fragments which cleave
badly or shatter when you try to cleave them to roughly equidimensional
shape. The crystallographer has to use what he gets, and what the
client supplies may be a gunge of material clinging to the interior
wall of a rotovap vessel, which decomposes or refuses to come out of
solution when you attempt to recrystallize it.
Tim Weakley, Chemistry, U. of Oregon
TWEAKLEY@OREGON.UOREGON.EDU
Why bother using DIFABS Analysis?
"You can use DIFABS in test mode at any stage, and it quite simple tells
you if there is a systematic trend to the residual as a function of orientation.
If the plot is fairly monochrome, then the residuals are not peaking up.
If there are bright patches, it means that there is a systematic trend to
the residual. Either FO or Fc is systematically wrong. Possible reasons
are:
- Absorption
- crystal damage (bending, shearing)
- anisotropic extinction
- mis-centering
- very anisotropic 'spot' shape (selective truncation)
- Application of unsuitable/ill-measured psi correction
(Use of DIFABS in 'test' mode to un-corrected and psi-corrected
data can help display the effect of the correction more clearly than just
looking at Rint)
- We have no evidence that missing atoms (eg solvent) lead to Difabs-like
effect"
Refer:
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