Subject: automatic solution of crystal structures : SIR92 & SIRPOW92

From: <[email-masked]>
Date: Wed, 12 Jan 94 15:11:55 GMT

Hi,

To all the crystallographers and others, I am a very satisfied
user of two programs (SIR92 and SIRPOW92)for automatic solution 
of crystal structures by direct methods, with a very nice graphic
interface.
The program for single crystal data produces (often with all the
atoms assigned and R<10%) input for two commonly used programs 
for structure refinement SHELX or CRYSTALS
For more information see below.

                            Davide Proserpio

To obtain a copy please contact Dr Cascarano providing your ftp
address.

Dr. Gianluca Cascarano
 Istituto  di  Ricerca per lo Sviluppo di Metodologie 
 Cristallografiche CNR, c/o Dipartimento Geomineralogico,
 Campus Universitario,  70124  Bari, Italy  
 phone +39-80-242624, FAX +39-80-242591
 e-mail  [email-masked]

*****************************************************************
SIR92 - A PROGRAM FOR AUTOMATIC SOLUTION OF CRYSTAL STRUCTURES BY 
DIRECT METHODS. 

A. ALTOMARE, G. CASCARANO, C.  GIACOVAZZO,  A. GUAGLIARDI
 Istituto  di  Ricerca   per   lo   Sviluppo    di    Metodologie 
 Cristallografiche CNR, c/o Dipartimento Geomineralogico,  Campus 
 Universitario,  70124  Bari,  Italy,  
M.C.  BURLA,  G.  POLIDORI
 Dipartimento  di   Scienze  della  Terra,   Universita',   06100 
 Perugia, Italy,  
M.  CAMALLI
 Ist.  di  Strutturistica  Chimica  "G.  Giacomello",  CNR,   Via  
 Salaria  Km   29,200,   00016    Monterotondo  stazione  (Roma),  
 Italy. 

THE CRYSTALLOGRAPHIC PROBLEM: Our recent developments  in  direct 
methods theory and in crystal structure refinement  persuaded  us 
to develop  a  fully  automated  structure-determination  program 
which is able to solve the phase problem  and  to  refine  atomic 
parameters in a single computer run.

METHOD OF SOLUTION: The  method  for   the   automatic  structure 
determination is based on the representation theory  (Giacovazzo, 
1977,  1980).  1-phase  structure   seminvariants   and   3-phase 
structure   invariants   are   estimated   via    their    second 
representation, 2-phase seminvariants and 4-phase invariants  via 
their first representation. SIR92 is the heir  of  SIR88  (Burla, 
Camalli, Cascarano, Giacovazzo, Polidori, Spagna & Viterbo, 1989) 
of which it retains most of  the  features  (f.e.,  treatment  of 
pseudotranslational symmetry, use of prior  information,  tangent 
weighting schemes, etc.). In SIR88 1-,2-phase  seminvariants  and 
positive estimated 3-phase invariants could be actively  used  in 
the phasing  process.  Negative  estimated  triplet  and  quartet 
invariants were used as a FOM together with psi-zero triplets. In 
SIR92 negative  estimated  triplet  and  quartet  invariants  and 
psi-zero triplets are actively used in the phasing process, which 
proved to be much more robust and efficient.  The  various  trial 
solutions can be obtained either  by  magic  integer  permutation 
(Main, 1978) or by random phases (Baggio,  Woolfson,  Declercq  & 
Germain, 1978). The best trial  solution,  selected  by  powerful 
FOM's, is automatically  processed  through  a  cyclic  procedure 
combining structure factor calculation - least squares -  2Fo-Fc  
Fourier synthesis. The final outcome is a set of  refined  atomic 
parameters  (x,y,z  and  isotropic  B  values)  associated   with 
suitable atomic species. The residual R value is  calculated  for 
user usefulness (final values usually between 0.08 and 0.15). The 
program runs in default when supplied with a  minimum  amount  of 
information (space  group  symbol,  cell  parameters,  unit  cell 
chemical content and  reflections)  but  documentation  has  been 
produced to allow the user to change default values. If a graphic 
device is available the user can follow  structure  solution  and 
refinement on the  screen.  In  the  final  stage  a  menu-driven 
interface is available in order to study molecular  geometry  and 
restart refinement. 

SOFTWARE ENVIRONMENT: The program has been  written  in  standard 
Fortran77. A module written in C language is supplied in order to 
interface the program with X-window or DEC-Window  terminals  for 
graphics. Therefore, besides the C compiler,  an Xlib library  is 
also needed. Two ASCII files are associated to the  program:  the 
first contains coefficients for calculating  scattering  factors, 
the second, necessary for graphics, contains on-line help. 

HARDWARE  ENVIRONMENT:  The  program  runs  on   UNIX   and   DEC 
workstations, on mainframe and on personal  computers  (for  this 
last one 4 Mbytes of RAM and a VGA monitor are needed). 

PROGRAM SPECIFICATION: The source code of the program consists of 
41.000 FORTRAN lines and of 2000 C lines (including comments).

DOCUMENTATION: Users instructions and program description  (about 
1500 lines) are supplied as an ASCII text file.

AVAILABILITY: The program is available free of  charge  from  the 
teams in Bari and in Perugia.  A  licence  agreement  has  to  be 
signed.

                            REFERENCES                           

Burla,  M.C.,  Camalli,  M.,  Cascarano,  G.,   Giacovazzo,   C., 
   Polidori, G., Spagna, R. & Viterbo, D. (1989). J. Appl. Cryst. 
   22,389-393.
Baggio, R., Woolfson, M.M., Declercq, J.P. & Germain, G.  (1978). 
   Acta Cryst. A34,883-892.
Giacovazzo, C. (1977). Acta Cryst. A33,933-944.
Giacovazzo, C. (1980). Acta Cryst. A36,362-372.
Main, P. (1978). Acta Cryst. A34,31-38.

*****************************************************************
SIRPOW.92  -  A  PROGRAM  FOR  AUTOMATIC  SOLUTION   OF   CRYSTAL 
STRUCTURES BY DIRECT METHODS OPTIMIZED FOR  POWDER  DATA.  

A. ALTOMARE, G. CASCARANO, C.  GIACOVAZZO,  A. GUAGLIARDI
 Istituto  di  Ricerca   per   lo   Sviluppo    di    Metodologie 
 Cristallografiche CNR, c/o Dipartimento Geomineralogico,  Campus 
 Universitario,  70124  Bari,  Italy,  
M.C.  BURLA,  G.  POLIDORI
 Dipartimento  di   Scienze  della  Terra,   Universita',   06100 
 Perugia, Italy,  
M.  CAMALLI
 Ist.  di  Strutturistica  Chimica  "G.  Giacomello",  CNR,   Via  
 Salaria  Km   29,200,   00016    Monterotondo  stazione  (Roma),  
 Italy. 

THE CRYSTALLOGRAPHIC PROBLEM:  Solving  crystal  structures  from 
powder data is not a routinary job: peak  overlapping,  preferred 
orientation  and  difficulties  in  background  estimation   make 
uncertain the evaluation of the diffraction intensities  for  the 
various  reflections.  Consequently  both  Patterson  and  direct 
methods  lose  efficiency   and   structure   solution   is   not 
straightforward. The first aim of this  program  is  to  optimize  
direct methods for powder data.

METHOD OF SOLUTION: The standard input of SIRPOW.92  consists  of 
lattice constants, space group,  chemical  content  of  the  unit 
cell, and a file of  reflections  as  provided  by  current  peak 
decomposition programs. Neutron data as well as X-ray data can be 
managed. The overlapping conditions, chosen  by  the  program  or 
fixed by the user, are stored for subsequent  use.  For  example, 
/E/'s of some "important" overlapping reflections can be suitably 
varied in order to generate different  phasing  pathways.  As  in 
SIR92  (Altomare,  Cascarano,  Giacovazzo,   Guagliardi,   Burla, 
Polidori  &  Camalli,  1994)  1-phase   and   2-phase   structure 
seminvariants  and  3-  and  4-phase  structure  invariants   are 
estimated via proper representations  (Giacovazzo,  1977,  1980). 
Trial solutions are obtained by the magic integer approach (Main, 
1978) or by random phases (Baggio, Woolfson, Declercq &  Germain, 
1978).  The  best  solution,  selected  by   proper   FOM's,   is 
automatically processed through a  cyclic  procedure  integrating 
structure factor calculation - least squares -   2Fo-Fc   Fourier 
synthesis. Due to reflection  overlap  the  observations  in  the 
least squares routine are the  total  intensities  of  groups  of 
reflections, while intensities of single  reflections  constitute 
single observations only when they do not overlap with any other. 
The final outcome is a set of refined atomic  parameters  (x,y,z) 
associated with atomic species. When neutron data  are  processed 
parameters of atomic species with negative scattering length  can 
also be determined. If a graphic device is available the user can 
follow structure solution and refinement on the  screen.  In  the 
final stage a menu-driven interface  is  available  in  order  to 
study molecular geometry and restart refinement. Due to the small 
ratio  "number  of  observations  /  number  of  parameters"  the 
residual R values  must  be  carefully  considered  by  the  user 
(usually final values between 0.06 and 0.20). 

SOFTWARE ENVIRONMENT: The program has  been  written  in  standard 
Fortran77. A module written in C language is supplied in order to 
interface the program with X-window or  DEC-Window  terminal  for 
graphics. Therefore, besides a C compiler,  an  Xlib  library  is 
also needed. Two ASCII files are associated to the  program:  the 
first contains coefficients for calculating  scattering  factors, 
the second, necessary for graphics, contains on-line help. 

HARDWARE  ENVIRONMENT:  The  program  runs  on   UNIX   and   DEC 
workstations, on mainframe and on personal  computers  (for  this 
last one 4 Mbytes of RAM and a VGA monitor are needed). 

PROGRAM SPECIFICATION: The source code of the program consists of 
44.000 FORTRAN lines and of 2000 C lines (including comments).

DOCUMENTATION: Users instructions and program description  (about 
1400 lines) are supplied as an ASCII text file.

AVAILABILITY: The program is available free of  charge  from  the 
teams in Bari and in Perugia.  A  licence  agreement  has  to  be 
signed.

                            REFERENCES                           

Altomare, A., Cascarano,  G.,  Giacovazzo,  C.,  Guagliardi,  A., 
   Burla, M.C., Polidori, G.  &  Camalli,  M.  (1994).  J.  Appl. 
   Cryst. 27,000-000.
Baggio, R., Woolfson, M.M., Declercq, J.P. & Germain, G.  (1978). 
   Acta Cryst. A34,883-892.
Giacovazzo, C. (1977). Acta Cryst. A33,933-944.
Giacovazzo, C. (1980). Acta Cryst. A36,362-372.
Main, P. (1978). Acta Cryst. A34,31-38.