MACINPLOT - a program to display electron density ... - IUCr Journals

Computer Program Abstracts The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and significant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should use the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. Cryst.

(1985), 18, 189-190].

J. AppL Cryst. (1990). 23, 141-142

MACINPLOT-a

program to display electron density and atomic models on the Macintosh personal comp u t e r . By T H O M A S J. S M I T H , Department of Biological Sciences, Lilly Hall of Life Sciences, Purdue University, West Lafayette, Indiana 47907, USA

(Received I August 1989; accepted 24 October 1989) The

crystallographic

problem:

Preparing diagrams of atomic models and electron density is tedious and time consuming using current software. The labelling and arrangement of the figure is difficult to manipulate and often requires hours of test plots and file manipulation. For instance, the font style and label positions are rigidly controlled and difficult to manipulate independently.

Method MACINPLOT

of

solution:

(Macintosh interactive ploting) is a program that reads plot files from the FRODO (1) graphics package (versions 6.1 and 6.6) (Jones, 1982), displays the figure on a Macintosh TM (registered trademark of Apple Computers), allows manipulation and labelling of the diagram, and copies the image as individual lines to upper RAM (the Clipboard) for easy transfer to any of the other Macintosh TM applications. This program supplements FRODO in the display of images for publication. It also allows users without sophisticated plotters to be able to present structural data easily. A plot file from the FRODO package is first read and reformatted on the mainframe supporting the graphics device before transfer to the Macintosh TM. This routine discards unessential information and allows the user to remove electron density that is not within a specified distance (in A) from any display atoms. Atomic models, electron density, and Mol. objects from FRODO can all be used. The resulting file is then transferred to the

COMPUTER PROGRAM ABSTRACTS

141

Macintosh TM. It should be noted that the current version of this program is not compatible with MultiFinder TM (registered trademark of Apple Computers), nor does it have the 'slabbing" function found in FRODO. Once the file is read into the MAClNPLOT program, the following options are available; (1) Display The atomic model, electron density and the Mol. object can be chosen individually for display. The figure can be displayed in mono or stereo. Mol. objects, electron density maps, atomic labels, distance line labels and distance lines can each be displayed in one of eight different colors if a color monitor or printer is available. The parameters that define a particular figure can be written out to a file any time during the execution. This allows one to re-enter the program where one left off, or to reset the various parameters during execution. These parameters include such things as the net rotation matrix applied to the initial coordinates, all labels and their positions, whether various Mol. objects, electron-density maps and atomic models had been turned on, and the colors for the various objects. One can also obtain a crude hard copy of the contents of the screen at any time during the execution. (2) Labelling For every atom displayed on the graphics, there are three pieces of information corresponding to it: the residue type, the residue number and the atom type. One can use any or all of this information (in any order) to label atoms. The atoms to be labelled can be chosen according to atom type or they can be 'picked' interactively with the mouse. One can also select/deselect atoms to be labelled by 'picking' them from a list of all atoms in the data file. Often in diagrams, the labels collide with the atomic models. Therefore, these labels can be given a global offset in both directions of the screen and/or they can be moved around interactively with the mouse (all the while maintaining the proper stereo depth). The labels can be displayed with seven different styles of lettering and 13 different font styles (if the fonts are available on the individual Macintosh TM system). The size of the lettering can be set to any integer value of a point size. (3) Scale and margins The stereo separation, the drawing size and the position of the image on the screen can all be adjusted interactively. (4) Measure and label distances Using the mouse, atoms can be selected and the distance between them measured. A line is drawn between the

two atoms, and the user is given the opportunity to type in a label which will correspond to the line. This label is put at the middle of the line (in all three dimensions) and its position on the line is maintained during all subsequent manipulations. As with other labels, these can be moved interactively with the mouse to alleviate obstruction. (5) Rotation The entire drawing can be rotated about the screen x, y and z axes.

0021-8898/90/020141-02503.00

(6) Pens The line can be changed to any thickness (in terms of pixels) for the atomic model, electron-density map(s), the Mol. object(s) and distance lines. Once the drawing is complete, one can then exit the program and use the Macintosh TM system to "paste' the diagram to files created by any other Macintosh TM programs such as word processors (e.g. MS Word 4.0TM; a registered trademark of Microsoft Corporation) and drawing programs (e.g. MacDraw IITM; a registered trademark of Claris Corporation). On color devices, the colors chosen in MAClNPLOT will be retained during the transfer process. Since the each line is an individual object, any standard graphics program (such as MacDraw II TM) can be used to edit drawings line by line, change individual font styles, colors, etc.

Software environment: The program that prepares the plot file is a very small program written in standard Fortran and runs interactively on the main frame that supports the graphics device (VAXTM; a registered trademark of Digital Equipment Corporation). There is no overlay structure nor any library routines called in this preparatory algorithm. The MACINPLOT program is written in Basic and can be supplied as the compiled executable and~or as the source code written with Microsoft Quick Basic TM (a registered trademark of Microsoft Corporation). The program was installed using Macintosh System version 6.0.2, and FinderTM (a registered trademark of Apple Computers) version 1.3. There is no overlay structure, and there are Macintosh TM ROM routines called during execution. Hardware environment: MACINPLOT has been tested on a Macintosh PlusTM, a Macintosh SETM, a Macintosh SE/30 TM, a Macintosh IICX TM, and on a Macintosh IIXTM. In the case of the latter, the large screen and faster computational speed are highly advantageous. A minimum of 1Mbyte of memory is recommended. The peripherals used are: Apple LaserWriter II TM, 3"5 in disk drive and/or 10Mbyte hard disk drive. For the Macintosh II TM family

© 1990 International Union of Crystallography

142

COMPUTER PROGRAM ABSTRACTS

with the Motorola TM 68020 microprocessor and/or the 68881 coprocessor, the program can be compiled specifically for these machines to improve greatly the computational speeds.

Program specification: MAC/NPLOTis totally interactive, using a combination of Macintoshra-style menus, buttons and mouse commands. It allows one to make diagrams, demonstrate distances and hydrogen-bonding patterns for manuscripts that are clear and unobstructed. With 1 Mbyte of memory, MACINPLOTcan handle about 2-3000 lines of input and can display up to 5-6000 lines with the stereo option on. Since the image is stored as individual lines in an array rather than as a bit image, the maximum number of characters that the array can contain is 32767. This hard limit is defined by the 16 bit processor and is the same for all of the Macintosh TM systems. A test data file of approximately 2000 lines is included. On a Macintosh Plus TM, this file takes approximately 3-4 min (real time) to be read by MAClNPLOT, and approximately 2-3 min are required per rotation. The drawing routine itself takes less than 30 s. An expanded Macintosh Plus/SE T M or a Macintosh II TM can easily handle large diagrams. MAClNPLOT has been tested on at least 30 files to date. One problem with the small screen of the Macintosh Plus/ SETM is that coordinates are rounded to the nearest pixel position, so that small errors in the diagram may occur. Therefore, it is advisable to create the desired diagram on the small screen then use the various options to expand the diagram and the font size greatly before exiting the program. One can take a diagram that it as large as several pages over to MacDraw IITM and then shrink it back down before laser printing it to obtain high-resolution lines and atom positions. On the large screen of the Macintosh IITM, diagrams that are several pages in size can be displayed in their entirety. The Fortran program used to prepare the plot file is about 120 lines long and is supplied as an ASCII file. The MACINPLOT program is approximately 2000 lines in length and can be supplied as a Microsoft Quick Basic TM file and/or as its compiled version.

Documentation: The write up for MAC/NPLOTis approximately 280 lines and can be supplied as an ASCII file or as a MS Word 4.0 TM document. A listing of the preparatory program and MACINPLOTcan also be supplied as a MS Word 4,0 document (although the line wrap around causes problems in

reading). It would be helpful if requests contained information as to what type of Macintosh TM the program might be used on so that all of the properly compiled versions can be sent. A v a i l a b i l i t y : Copies of the program can be obtained by writing to the author. The program and documentation will be supplied on a 3-5 in doublesided, double-density floppy disk formatted for the Macintosh TM. A nominal fee will be charged to cover the cost of the disk or a blank disk can be sent with the request.

Keywords:

Plotting, Macintosh TM, FRODO.

graphics,

Reference Jones, T. A. (1982). In Computational Crystallography, edited by D. Sayre, pp. 303-317. Oxford: Clarendon Press.

J. Appl. Cryst. (1990). 23, 142-143

SGROUPa program for determination of possible space groups from structure-factor l i s t i n g s . By J. YERKESS, Computer Centre, University of Bradford, Bradford, West Yorkshire BD7 1 DP, England (Received 26 July 1989; accepted 8 September 1989) The

crystallographic

problem:

The determination of space groups from observed patterns of systematic absences may be prone to error, particularly with high-symmetry space groups where the absences are relatively complex and where several space groups may have the same absences. In cases where diffractometer data collection has not been preceded by photographic examination, there is also the possibility that some absences may be overlooked.

Method of solution: The program reads a file of data (e.g. from a diffractometer data collection), where each record consists of the Miller indices h,k,I and the structure factor (or intensity) and its standard deviation, for each measured Bragg reflection. Any reflections with one or more indices outside the range for which the program is coded are discarded. Subsequent analysis may be based on either the entire remaining list of reflections or only on those with structure-factor magnitudes or structure factor/standard deviation ratios greater than a specified minimum.

0021-8898/90/020142-02503.00

The set of reflection indices is first tested for systematic absences due to lattice centring in the order F, I, A, B, C. When a reflection is found which violates the required absence criterion for the lattice type under test, that lattice type is rejected and the test commences for the next type. If no violation is found, the lattice type is accepted and tests for the remaining types are not made. If all centred lattice types are rejected, the lattice is assumed to be primitive. Tests are next made for absences due to symmetry elements, in the following order: d-, n-, a-, b-,c-glide planes 4-fold, 2-fold screw axes hhl etc. absences for / ~ 2n hhl etc. absences for ( / + h) m 2n hhl etc. absences for (2h + / ) ~ 4n. Finally, the detected absences are matched against the expected absences for each space group of the established lattice type in the cubic, tetragonal, orthorhombic, monoclinic and triclinic systems with the standard settings from

International Tables for Crystallography (1983). All space groups which either fully or partially match the detected absences are regarded as acceptable. Thus, space groups which have no absences will always appear on the list of possibilities. The present version of the program does not include tests for trigonal and hexagonal space groups. The output from the program consists of a list of the detected absences (or a note of the first reflection found to violate an absence criterion) followed by a list of the possible space groups in decreasing order of space-group number. S o f t w a r e e n v i r o n m e n t : The program is written in standard Fortran 77 and has been implemented and fully tested under the CDC NOS operating system. Before compilation, the minimum and maximum values expected for the Miller indices must be set by the user. No external libraries are required. The program has also been run successfully under the CDC NOS/VE, the APOLLO AEGIS and the IBM VM/CMS operating systems. It should be easily portable, with minor modifications, to any system which has a Fortran 77 compiler.

Hardware environment: The program is implemented on a CDC Cyber 180-830 dual processor with 2 million words of memory (one word = 60 bits) at the University of Bradford Computer Centre. With optimized compilation and segmented loading, the binary object program requires 41400 words of

© 1990 International Union of Crystallography