SDPD Internet Course
Frequently asked questions
Questions about :
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1 - Yesterday,
I got a mail from a Ph.D student asking me whether I can provide him the
tutorial materials (as he can not pay the tutorial fee, which is quite
high with respect to his country standard of living). I certainly shall
not mind to share my knowledge. But before that I would certainly like
to know whether the distribution of these materials are going to violate
any copyright law or any such illegal things, which can put me into trouble
later. Please let me know.
2 - I
am a graduate student from India and I wish to attend your course on the
structure-determination from powder data, but I was quite disheartened
by the fees mentioned in the web-page. The fees of 1625 French Franks,
is far too much in my currency Indian Rupees. It is nearly 12500 Rs. which
is my stipend for three months and I cannot afford that kind of money.
I'm not sure that if it would be right on my part to ask for a concession
in the fees. In case I cannot take the diploma and If I wish to still attend
the course via e-mail, is it possible to do so? I would be just happy to
learn even in the absence of a formal DIPLOMA awarded by University du
Maine. I request to kindly consider my case and help me in learning by
sending the study material. It would be very kind of you and a great help
if you can e-mail me the course-work material. I already have finished
my masters degree and have done a basic course in crystallography. Looking
with great hope to hear from you.
3 - Just
a note to let you know that I am still alive and continuing with the course.
However, this academic semester has turned out to be unbelievably busy
and I have little time for learning and/or doing any science. I hope to
get something new back to you soon and apologize for being such an intermittent
4 - I
sent a check to the Agent Comptable for the SDPD course last thursday.
Please let me know when it arrives because I want to begin the course as
soon as possible.
5 - I
am going to pay off the SDPD Internet Course registration by bank transfer
today. The administration of the University asked me your tax department
number. It´s the Fiscal Identification Number (NIF) in Spain.
am experiencing difficulties decompressing the zip files needed to proceed
successfully with the sdpd - course. I have downloaded both 'netzip' and
'Quicktime', but together with University decompression software I just
get an infinite amount of netscape browser windows being opened. Please
could you tell me where I am going wrong (if at all!) and how I can remedy
this problem ?
wish to finish my course in 3 months. Do you think this will be possible
1 - I
don't have the PDF-2 database. HELP !!!!!!
2 - I
was using EVA, and found out that apparently, stripping of K_alpha2 line
may not matter on the search process. Is it correct ? Then, is it necessary
to strip off K_alpha2 line before searching, or only the background correction
3 - In
the first weeks's solution, you have given some compounds with indexing
numbers such as 71-1231, 83-1237, and so on. Here, we are not aware of
any indexing above 47-****. Are these indexing from your personal data
base ? I was told that one can have personal data base also, but that will
start with 90-****.
to propose a fictitious cell corresponding to the harmonics if you do not
know any cell parameter ?
- There is not other version of CELREF for normal screens
- What is the mathematical relationship between the so-called
direct cell and the reduced cell ?
manual suggests that peak position should be searched BEFORE background
substraction. I think it is improper. What is your opinion ?
is a reasonable strategy for choosing the 20-40 lines to be indexed: should
they be the first 20-40 ? or should they be the most intense ?
PDF database I have is from 1996, and there I could not find the card for
the NAC compound. Could you send me the data for it ?
used the data-2 including peaks from standard sample. I have no idea about
what I should do with data-1.
1 - How
reasonable it is to use Crysfire zero-shift ? I think it is more reasonable
to crosscheck with CELREF/ERACEL.
2 - How
to propose a cell when you get a lot of solutions ?
1 - I
have a problem with DMPLOT. The version that I got from the zip-file armel.zip,
does not write the background in the file background.dat. The other version
I have is that obtained from the file dmplt348.exe. In this version the
program does not understand the correct range of the DRX pattern. For example,
when I ask to read the file na5.rit, it takes the 2theta range between
10 and ~105 degrees (when it should be 10-150 dg.) I have tried every thing
I could but without success. Could you help me?
2 - I
wish to know how to decide the initial values, especially, scale, U, V,
W., in structure factor extracting. I tried with the naoxa0 (Na/COO) files(copied
from the tutorial) with fp90: I can not repeat the 2nd step. I got an error
message "square of FWHM<0 at 2 theta/TOF: 125.0", I wish you could teach
me what does this mean, and how to correct this kind of problem.
please find my answers to session 5. However, I'm wondering why the Sigma
of |Fobs| are so big. Is there anything wrong ?
PDF card I have for CrF3 is the one with number 16-0044 (since
my PDF database is from 1993). May be you have a more recent one. If yes,
could please send me a copy of it ?
think I have finally worked out how to extract the data about CrF3
from the database in the correct spacegroup and I have generated a simulation
in Fullprof. However, I think I must still have done something wrong as
the amount of impurity in either pattern sent seems very small and so estimating
the zero point is difficult/impossible and when I've tried to let Crysfire
do the estimation and then find the cell, no sensible solutions seem to
1 - I've
not been able to view the structures with STRUVIR. There was no warning
message from STRUVIR with the .dat file (Na5test.dat). But no structure
could be viewed. It seems that i'm having the same problem with the .dat
file copied from the SDPD tutorial : http://www.cristal.org/iniref/tutorial/naoxa11.html
Please help me to find out what's the
problem for both .dat files.
2 - I
wish to know in extracting structure factors by Fullprof: What's ground
for deciding following parameters :? Wdt, R_at, R_an, R_pr, R_gl.
1 - I
am not sure what kind of result you are expecting from this session's work.
The solutions I am getting all seem a bit unstable and so I was wondering
if you could let me know what is a usual result.
1 - I
was wondering if you could give me some more help for this week's work.
I have managed to work out the space group and cell parameters however,
I couldn't, unsurprisingly, find a stable solution from SIR97 or SHELX97.
I then tried Espoir using Prespoir to set up the .dat file. Again no sensible
solution has been found despite numerous attempts changing different parameters.
I was wondering if you could point out where I have gone wrong. I think
that it is maybe in the section below:
! maximum moves for each type of atom
! annealing law, sigma, reject
2.0000 1.0000 0.0010
! number of events for : print, maximum, save
20000 200000 100000
! events for restart, rmax, ichi, number of runs
40000 0.200 2 10
The manual doesn't seem very clear on
how you should determine values for these parameters so any help that you
could give would be greatly appreciated.
2 - I
have finally managed to get a reasonable result with ESPOIR. Although the
fragment was relatively easily located, the O and methyl group were less
easy to sort out. I'm not sure why, but with exactly the same .dat file,
I got two different results, the non windows gui giving a non-reasonable
I was wondering if you could give me any more guidance on how/why you pick
the initial numbers if events, rmax, ichi and number of runs as this seems
to make a difference and yet seems to be random.
then I cannot obtain RpF values lower than 46%. The final values are exactly
the same as the input values. Can you kindly suggest me on how to improve
this by ESPOIR ? Is there something wrong in my input file ?
The best R I got was 0.157. I noticed that different run seemed giving
different final atomic coordinates. I'm wondering why ?
- Redistributing the Course material would certainly be illegal.
Even more illegal (if possible ;-) if you redistribute the material for
some fees. I don't want to know what you will do...
- Thank you for your interest in the SDPD Internet Course. You
are not the first to ask it for free. A large part of the documentation
is in free access, so that you may follow it by yourself at :
You will find there exercises
with correction, lists of software, references. But you will not have access
exercises without correction
and to the interactive help which are part of the commercial course, sorry.
- The course is not limited in time. You may go back at your
convenience. Best regards, and don't kill yourself at work !
The best is to begin immediately because administration poor efficiency
will cause certainly time lost.
I guess the name is TVA identification number here : FR66197209166,
Université du Maine.
You will find possibilities to download Winzip at : http://www.winzip.com/ddchomea.htm
I hope this will be possible. However, Nobody succeeded in finishing the
course in 12 weeks, up to now. The knowledge to acquire is quite large
so that the fastest students needed 5-6 months. Nevertheless, they were
not doing only the course during that time.
OK, let us wait for your session-1 solutions when it will be possible,
and start already the session-2. Only session-1 needs a commercial product
(PDF-2 and a search-match software), so that you should not have other
problem of this kind (but PDF-2 is certainly needed for becoming a SDPD
expert). If you receive PDF-2 before the end of the course, you will try
to identify the session-1 materials. No lab at your university having PDF-2
- I had the same experience. It should even be possible to obtain
some match without background subtraction. I have never seen any study
comparing the performances with and without K_alpha2 stripping. Probably,
the reason that both work well is the absence of clear separation between
the two components at low angle, where matching is the most important.
But it is so easy to perform the corrections that I prefer to do it every
- This means the you do not use the latest version of ICDD which
has included powder patterns calculated from the ICSD database. In that
new version (since 1998 in fact), there are >120000 patterns. Have a look
at your ICDD CD-ROM. May be the data prepared for EVA were not updated
? Those data are .cat files if I remember well. They are prepared for EVA
by PDFMAINT from the ICDD CD-ROM, I think (not sure).
It is to you to decide if you have located one or several series of harmonics
from your data. For instance, if you have d = 12.6, and also d = 6.3 and
d = 4.2, then you may suspect that they built a series of harmonics. Why
not the 100, the 200 and the 300 reflections ? So that you have now one
of the three fictitious cell parameters with a = 12.6A. Then search for
b and c with 2 other series of harmonics. You will be then able to refine
The old (DOS) version of CELREF is still distributed with the name ERACEL
and the new version with graphical user
interface is at : http://www.ccp14.ac.uk/tutorial/lmgp/celref.htm
reduced cell is the unit cell with the smallest volume whose axes are the
three shortest non-coplanar translations in the lattice (official definition).
- I always subtract the background and correct for K-alpha2
before searching for peak positions. However, the result could be very
similar if you remove K-alpha2 and then search for peak positions without
subtracting the background. I prefer the first option, but the second may
have advantage that less errors are introduced if the background is not
removed. A kind of no-yes no-no answer...
- The fact is that untill you do not obtain an evident proposition,
you may have to test with various data sets (including or not some weak
reflections). The first data set to be used should not contains too weak
reflections in my opinion. You should also be careful about possible artifacts
near of very intense reflections which could be generated by the K-alpha2
elimination process (there is frequently a 1% false reflection after the
100% one). Indexing is more an art than a science you know. About the biesrf.rit
case : the biggest experts have broken their teeth on it, it remains unsolved.
- Well, you should have it because it is the 36-1496. However,
the card is a bit wrong. The 84-1651 is the good one, calculated from the
ICSD database (you should update your PDF-2 database for obtaining it).
But you do not need that card. All you need is the list of hkl and d(A)
values. The week-2 course material gives you all you need for being able
to calculate them : you have links to programs which can calculate reflexion
positions, and the NAC cubic cell parameter is given together with the
space group in the exercise : a=10.2533A, space group I213
- It is true that data-2 is sufficient for solving the problem.
Nevertheless, it may occur
that peaks from the unknown are masked by peaks from the standard. In such
a case, it is
possible to extrapolate the
zeropoint from the unknown + standard pattern to the pure unknown pattern,
and to index from peak positions from the pure pattern. You will see that
in the official correction.
You mean that crysfire has an internal possibility for zero shift estimation
? Seemed to me that the user had to give a value (from a previous estimation,
involving a standard or the harmonics method). Some programs inside Crysfire
may propose a post-indexing zeropoint, produced after cell parameters refinement
(ITO does that). But it is certainly preferable to have a good idea of
the zeropoint BEFORE to use Crysfire.
Comments from Robin Shirley about that
"You mean that crysfire has an internal
possibility for zero shift estimation ?"
Yes, Crysfire (or at least its front-end
program CRYS) does indeed have facilities for Z2Th (2Theta zero correction)
estimation, primarily by self-calibration from lines and their second orders.
In CRYS v9.34h (Crysfire 2000 - i.e. the
July 2000 release), this can be used either directly for Z2th (the
default option: Z) or now for specimen-displacement ratio (new option:
1) Option Z is appropriate for parallel
beam geometry, and in
principle for any constant residual that
remains after a specimen-displacement correction has been applied correctly.
2) Option T is more appropriate for the
convergent-beam geometry (Bragg-Brentano,
3) Linear recalibration is also possible
as an option at the end of an obs-calc pattern comparison within CA.
However, this can only be used when a trial cell is available, and is now
superseded in many cases by self-calibration for specimen displacement.
Of course the determination of these correction
parameters in the course of a Rietveld-method refinement or other full-profile
process is more reliable (though this may require more information than
initially is available).
Well, the difference is made on the Figure of Merit (FoM)
which should be the highest possible,
and at least > 20. Your best FoM are <13. I don't know what could be
the error you made. I hope you will see where was the error by
looking later at the official corrections
(sign of zeropoint ?). Another way to test a cell proposition is to extract
structure factors by a cell constraint
method. The profile
reliability Rp factor should be as low
as possible (<10%).
This is the subject of session 4.
In fact, the background is written in the file backgrnd.xy by default,
and, if you try to give another name, it should not have more than 8 characters
before the . (this is old DOS program...). If all that fail, then you may
use the classic DMPLOT by cutting the pattern in 2 pieces of less than
In structure factor extracting mode, there is no scale to refine. You have
to fix it to an arbitrary value, say 0.01. If the extracted structure factor
amplitudes in the .fou file are too small (using Fullprof), then you may
consider to decrease that fixed scale factor at 0.001 or 0.0001 or less.
Try to obtain the "|Fobs|" max near of 500-1000.
About the U,V,W, they enter in the FWHM
formula by U tan**2(theta) + V tan(theta) +W. So that, either you already
know your diffractometer performances and have a set of starting U, V,
W or not. If not, the best is to start by U=V=0 and select W as 0.01 for
instance. See what happen in a few refinement cycles. Refine V and W. And
finally U, V, and W, but this may be difficult if your data do nor go far
beyond 90° 2theta. Anyway, the old FP90 Fullprof version is more stable
than the recent WinFullprof when extracting structure factors. You should
perform a few cycles at the beginning without refining nothing but the
zeropoint maybe. This supposes that your cell parameters are already very
good, and also that your profile parameters are not too bad. Otherwise
you may encounter that problem with FWHM <0. because some parameters
The ESD for the "|Fobs|" as extracted by WinFullprof, have not a lot of
meaning. The previous fp90 version of Fullprof gave even higher ESDs. Remember
that they are absolutely not used by any Direct or Patterson method program,
but for elimination of the too bad data. A program like OVERLAP takes these
values and change them with ESD="|Fobs|"/100.
2 - There
is not more recent one. And the data in the Wyckof book or in the ICSD
database are also very old with quite bad cell parameters. This is one
difficulty of the exercise... The best is that I give you the cell parameters
of a CrF3 sample made at the Fluoride Lab : a = 4.977 A, c = 13.145
A , space group R-3c, hexagonal setting. isostructural with FeF3, VF3,
etc. You may use HKLGEN in order to generate the list of hkl and their
angular positions (or another program).
About CrF3, the impurity in the session 5 exercise, you
may have noticed that there were available
only old published data including rather wrong cell parameters. This is
probably the origin of your problems. However, I recommend you to first
print a drawing of the powder patterns. If you had examined more carefully
the two patterns, one with less impurity than the other, you would certainly
not have concluded that both mixtures were containing very few CrF3
impurity... Powder diffraction expertise has a visual part : looking first
and carefully at the patterns allows to avoid many traps.
I think that your problem is just that the EOF character (End of Line)
is placed at the end of the O2 line. It should be at the beginning of the
last line. So that you have to make a "return" at the end of the O2 line.
This is the most common error with many programs reading data file. In
that case, the O2 line is ignored, and the program cannot find any polyhedron.
WDT = width (range) of calc. profile in units of Hk (typically 3.5 for
Gaussian and 10 for Lorentzian, 3-3.5 for T.O.F.).
For Rietveld application or for extracting
structure factors, the
same kind of values will apply. For X-ray
case, profile shapes
are generally lorentzian-like, and for
neutron data, they are
Gaussian-like. You may find useful to
increase the suggested
Wdt values above, if you see staircase
steps on each side of
the calculated profiles. Values of Wdt
up to 15 or 20 may become necessary sometimes.
The R_at, R_an, R_pr, R_gl are the relaxation
factors. They are used for damping the shift on the refined parameters.
The shift is multiplied by the R_ value, so that this may reduce unstability
effects on some parameters. R_at is for atomic parameters : coordinates,
magnetic moments, site occupancies & isotropic displacement (temperature)
factors. R_an is for anisotropic displacement (temperature) factors. R_pr
is for profile parameters, asymmetry, overall displacement (temperature),
cell constants, preferred orientation parameters, strains, size, propagation
vectors & user-supplied parameters. R_gl is for global parameters,
zero-shift T0, background, displacement and transparency.
For a very good pattern with many reflections,
going to large angle, and few refined parameters, there is no reason to
damp any parameter, so that all R_ values could be set to 1. But in many
cases, if you identify one or several parameters fluctuating, if not diverging,
then those R_ parameters will help you to smooth the fluctuations. In case
of extracting structure factors, it is recommended to apply a large number
of refinement cycles (10-40) when the K-alpha 1-2 is present.
So that, using R_ values as low as 0.2
may be decided, in a preventive manner (just in case some parameter is
1 - Structure
solution does not provide always a complete model. This is why the week-7
exercises text concludes by : "Give your final best list of atomic coordinates
together with the reliability factors." Just send me the complete
result and you will see probably in the official correction that your result
is already a "usual result".
! maximum moves for each type of atom
This is certainly not enough : your molecule
will not be allowed to move more than +-0.5 angstrom from its initial position.
You should select values at least equal to half the largest cell parameter.
This is probably the main reason for unsuccess. The molecule had not any
chance to attain the right place.
! annealing law, sigma, reject
2.0000 1.0000 0.0010
The reject term (0.001) may be too low
for any event not improving the fit to be accepted. So that you may fall
in a false minimum.
! number of events for : print, maximum,
! events for restart, rmax, ichi, number
40000 0.200 2
This may be OK. Increase rmax to 0.3 or
0.35 would be better for not stopping all test too quickly (at 40000 Monte
Running 2 times or 3 times the program with the same data will give 2 or
3 sets of different results. That is Monte Carlo. If the success ratio
is 1/50, you may have to perform several runs of 50 tests for obtaining
the best result. In that case, the pyrene molecule is located in every
test with R ~20% (by the way, you did not gave me your best R factor).
But the 2 last atoms are more difficult to locate. Once located,
they will provide R ~10%.
May be it is not clear that nstart and rmax are parameters used to avoid
wasting time in calculations that will not provide a solution. But in fact,
there is no proof that this supposition of "if R is still larger than
Rmax after nstart Monte Carlo events, no good solution can be expected"
is really is good supposition... You may find more satisfyng to discard
none of the tests before their normal end by using nstart=n2. That should
be your choice. I understand that ESPOIR may be surprising as a program
for finding a solution. it needs long time, many runs and many tests in
a run. It looks very inefficient but sometimes can provide results when
classic methods fails. I hope you are convinced ;-). SDPD is much more
difficult than structure determination from single crystal data. It needs
much more efforts. ESPOIR is typical of this need for trying again and
again before to give up.
Yes, there is something wrong. But your error is understandable. When using
the Molecular replacement method, the coordinates defining the molecule
have to build the complete molecule : the atoms cannot belong to different
molecules inside the cell. Rotations and translations are made around the
gravity center of the group of atoms entered, and will destroy the
original atom packing if the coordinates are those of atoms in different
molecules. In fact, this is the fault of ESPOIR itself which produces some
+1 or -1 additions to the coordinates for the final output. So, if you
want to reuse those coordinates, you have first to verify if the original
molecule connectivity was not broken. This is made fast by using ORTEP
on the .res file, for instance. But, anyway, you will not obtain much better
result than your 25%. Completing that result will be the scope of half
the week-10. So, be patient. You may guess that this will need to apply
some Rietveld refinement. Going further with the originally extracted "|Fobs|"
is not possible, you attained the limit.
5 - The
difference may only be an apparent difference. There are 4 molecules inside
the cell, so that ESPOIR may propose the 4 possible positions. Moreover,
several origins are possible by choosing any of the inversion centers,
and this will also produce apparently different coordinates.
Updated September 15, 2000.