New SHELX97 Homepage at http://linux.uni-ac.gwdg.de/SHELX/

[Lachlan Cranswick]

Posted to crystallography mailing list(s.t.xtal_l at ill.fr)/
          general crystallography newsgroup (sci.techniques.xtallography)
          rietveld mailing list (Rietveld_l at ill.fr)
          biological crystallography newsgroup (bionet.xtallography)

The new Shelx Homepage is at:
    http://linux.uni-ac.gwdg.de/SHELX/

This describes the latest version of shelx and includes a link to
the application form at:-
    http://linux.uni-ac.gwdg.de/SHELX/applfrm.html

----

Sort of paraphrasing the Website:
SHELX-97 is currently available by ftp transfer, on 100MB ZIP diskettes 
and on CDROM. It is free to academics (small donations are however not 
refused) and for a license fee of US$2499 to for-profit organizations.
Academic users who request the programs on CDROM or ZIP diskettes are 
expected to contribute US$99; this may be waived for poorer countries 
without adequate ftp access. Applications should be made by post or by 
fax using the following application form only.
   http://linux.uni-ac.gwdg.de/SHELX/applfrm.html

The application form (which has to signed and mailed or faxed) includes 
such information as:
   Please tell me how to obtain SHELX-97 by ftp [ _ ]; 
   I already possess a copy of SHELX-97 [ _ ]; 
   Please supply it on CDROM [ _ ] / 100MB ZIP diskette [ _ ]; 
   [ _ ] I agree to cite SHELX-97 in all publications for which it was useful; 
   [ _ ] I agree that the author has no liability for any damage or 
           loss caused by the programs; 
   [ _ ] Please send me a receipt for enclosed cheque; 
   [ _ ] Please send me an invoice; [ _ ] Please send direct bank transfer info; 
   [ _ ] No payment required (academic/ftp; $99 for academic users if CDROM or ZIP) 

----

9. Support and bug reporting 

The author is happy to provide advice by email
(gsheldr at shelx.uni-ac.gwdg.de) or fax (+49-551-392582) but
not phone. Questions already answered in this file or in the full
documentation may be moved to the bottom of the pile! In
particular he would like to be informed of any suspected bugs in
the programs or of errors or lack of clarity in the documentation;
the current release has benefitted enormously from such
contributions by users. 

Important announcement about new versions etc. will be posted
on the crystallagraphic email newsgroups bionet.xtallography and
sci.techniques.xtallography; these may also be used by users for
a more general or critical discussion of the programs. The
SHELX beta-test newsgroup will now be wound up.

------

Following is the part of the web page dealing with the existing FAQ 
and changes from Shelx93 to Shelx97 information.

Cheers,

Lachlan.

Lachlan Cranswick                                            _--_|\  
Phone/Fax : (613) 9455-1345                                 /      \
E-mail : lachlan at melbpc.org.au                              \_.--._/
Mobile Phone/Voice Mail : 0412-1141-31                            v
Crystallographic WWW : http://www.unige.ch/crystal/stxnews/stx/volnteer.htm 

------


7. Frequently asked questions 

Q1: Please send me a copy of SHELX-76. I am afraid that I
cannot use the new version because my diffractometer measures
F-values, not intensities. 

A: Buy a CCD detector. They measure intensities! In fact,
diffractometers measure intensities too. You just need the right
data reduction program. If you are desperate you can even feed
SHELXL with F-values using HKLF 3. 

Q2: When I start SHELXL on my PC the disk rattles loudly for
several hours and smoke comes out of the back. Is this a bug? 

A: You must be trying to run SHELX under some version of
WINDOWS! The best solution is to reformat the hard disk and
install LINUX. If you are running WINDOWS-95 an inferior
alternative is to 'Reboot to DOS' (as recommended for games
programs). 

Q3: The referee rejected my paper because the weighted
R-factor was too high and because the stupid program had
forgotten to fix the y coordinate of one atom to fix the origin in
space group P21. What should I do? 

A: Try another journal; if you emphasize the 'biological
relevance' enough, they may not notice the R-factor! Note that
wR2 (based on intensities and all data) is of necessity 2 to 3
times higher than wR1 (based on F and leaving out reflections
with say F<4sigma. Unfortunately SHELXL cannot work out
wR1, because the weighting scheme for intensities does not
apply to F-values. It is better to quote the unweighted R1 (with
or without a 4sigma threshold) anyway, because it is too easy to
cheat on wR2 by modifying the weights! It is no longer
necessary or desirable to fix the origin by fixing coordinates, the
program applies appropriate floating origin restraints
automatically when they are needed. 

Q4: The program tells me to refine extinction, this does reduce
the R-factor but the extinction parameter becomes very large
lthough my crystal could hardly be described as 'perfect'. Is this
reasonable? 

A: No. The most likely causes of large apparent extinction are:
(a) you have input F with HKLF 4, (b) A few reflections that
should be very strong have been measured as weak because
they were cut off by the beam-stop, (c) your counter was
saturating and an inadequate dead-time correction was made (in
the case of an image plate this is an 'overload'), or (d) your
counter was defective or the energy discrimination was set
wrongly. Overloads may be eliminated by 'OMIT h k l' if
necessary. 

Q5: The structure could only be solved in P1, not P-1, but on
refinement some of the bond lengths and U-values are wildly
different in the two molecules. If I use SAME the geometries of
the two molecules become very similar but how do I restrain the
Uij components of equivalent atoms to be the same? 

A: You could use EADP, but it might be better to look for the
inversion center instead, otherwise you will probably be
'marshed'. 


Q6: I included batch numbers in the .hkl file and BASF
parameters in the .ins file, but the stupid program still didn't refine
the batch scale factors!? 

A: You need MERG 0 (the default MERG 2 will average the
batch numbers). 

Q7: How do I obtain the molecular replacement program
PATSEE? 

A: PATSEE has been maintained by its author, Ernst Egert,
since he moved from Goettingen to the University of Frankfurt.
He can be contacted by fax (+49-69-7982-9128) or email
(bolte at chemie.uni-frankfurt.d400.de). 


Q8: What should I do about 'may be split' warnings? 

A: Probably nothing. The program prints out this warning
whenever it might be possible to interpret the anisotropic
displacement of an atom in terms of two discrete sites. Such
atoms should be checked (e.g. with the help of an ORTEP plot)
but in many cases the single-site anisotropic description is still
eminently suitable. 

Q9: I get the message ' ** UNSET FREE VARIABLE FOR
ATOM ... **' but I haven't used any 'free variables'!? 

A: There is a typo in your atom coordinates, e.g. a decimal point
missing or replaced by a comma. 


Q10: After using SHELXPRO to prepare the .ins file from a
PDB file and then running SHELXL, I get the message: ' ** No
match for 2 atoms in DFIX ** ' !? 

A: This message probably refers to the fact that SHELXPRO
labels the oxygens of the carboxy-terminus OT1 and OT2 so
that special restraints can be applied, so there is no atom called
'O' in this residue. This is normal and can be safely ignored.
Other similar messages, also messages about bad CHIV or
AFIX connectivity, should be investigated (by checking the extra
information, including the connectivity table, given in the .lst file)
to see if they can be ignored safely or not. If the initial geometry
is poor, it may be necessary to edit the automatically generated
connectivity table with BIND and FREE. 

Q11: The program prints out a Flack x parameter of 0.3 with an
esd of 0.05. Is the crystal racemically twinned? 

A: Not necessarily! The Flack parameter estimated by the
program in the final structure factor calculation ignores
correlations with all other parameters (except the overall scale
factor). Since these parameters may have refined so as best to fit
a wrong absolute structure, it is quite possible to get an estimate
of about 0.3 for the Flack parameter when the true value is 1,
i.e. the structure needs to be inverted and is not racemically
twinned. On the other hand a value close to zero with a small
esd is a strong indication that the absolute structure is correct. If
there is any doubt the Flack parameter should be refined
together with all the other parameters using TWIN and BASF. 


Q12: Neither direct methods nor Patterson interpretation in
SHELXS can find the 24 selenium atoms from MAD data of my
selenomethionine labeled protein. 

A: I'm not surprised. 

Q13: How does one set up restraints for a non-standard residue
in a protein for SHELXL? 

A: First find a suitable fragment in a database such as the CSD,
then calculate all 1,2- and 1,3-distances and turn them into
DFIX and DANG instructions resp. FLAT and (zero chiral
volume) CHIV restraints can easily be added by hand. If the
structure contains a number of identical units such as sulfate ions,
SADI or SAME can be used instead, then it is not necessary to
invent any target values. 


Q14: What is the worst resolution that is acceptable for: (a)
solution of a structure by direct methods using SHELXS, (b)
refinement with SHELXL? 

A: Direct methods assume randomly distributed resolved atoms.
Direct methods are crucially dependent on having atomic
resolution data, say better than 1.2A. A good rule of thumb is
that a least one half of the theoretically possible number of
reflection s between 1.1 and 1.2A should have been measured
with I>2sigma for direct methods to be successful, though this
rule can be relaxed somewhat for centrosymmetric structures
and structures containing heavier atoms. In particular the
resolution is not so critical for the location of heavy atoms from
delta=F data, provided that the minimum distance betwen heavy
atoms is much greater than the resolution. SHELXL lacks the
energy terms used by e.g. X-PLOR for refinement against
low-resolution data. This imposes an effective limit of about
2.5A for SHELXL refinement, but this limit may be extended a
little to lower resolution if NCS restraints can be used. 

==========

8. Important changes since SHELX-93 and SHELXS-86 

1. The new programs SHELXPRO (interface for protein users),
SHELXWAT (automated water divining for macromolecules)
and SHELXA (post-absorption corrections) have been added.
The full documentation should be consulted for details. In
particular, SHELXPRO includes extensive facilities for data
input, analysing refinement results, PDB file manipulation and
deposition, and preparation of maps for graphics programs such
as O. SHELXPRO replaces the program PDBINS supplied
with SHELXL-93, and the dictionary file SHELXL.DIC that
PDBINS used is no longer required (an improved dictionary is
stored internally in SHELXPRO). 

The program SHELXA has been kindly donated to the system
by an anonymous user. It applies "absorption corrections" by
fitting the observed to the calculated intensities as in the program
DIFABS. SHELXA is intended for EMERGENCY USE
ONLY, eg. when the world's only crystal falls off the
diffractometer before there is time to make proper absorption
corrections by indexing crystal faces or by determining an
absorption surface experimentally by measuring equivalent
reflections at different azimuthal angles etc. Under no
circumstances should the results be published; the anonymous
donor does not wish to be cited in this non-existent publication
because it might ruin his reputation!

A simple program SHELXWAT has been added that iteratively
recycles SHELXL to provide automatic water divining. This may
be regarded as a cheap and inadequate imitation of the ARP
method [V.Lamzin & K.S.Wilson, Acta Cryst. D49 (1993)
129-147], but is relatively easy to use and useful if you intend to
take a holiday. 

A large version of SHELXL called SHELXH has been added
for the refinement of large structures (on fast computers with a
lot of RAM). 

2. The new version of SHELXS includes the 'phase annealing'
direct methods described in Acta Cryst. A46 (1990) 467-473,
and the Patterson interpretation method used in Acta Cryst. D49
(1993) 18-23. The latter represents my best method so far for
finding heavy atoms from macromolecular SIR and OAS data,
although it was originally written for small molecules. Examples
are provided for small molecules (log, cumos2) and protein SIR
data (barnase). The location of more than ca. 10 selenium atoms
from noisy MAD data remains a difficult problem that I am still
working on! 

[post terminated]