VM - System call

PURPOSE

To access the operating system from SPIDER using a system (Unix) command.

USAGE

.OPERATION: VM

<or> VM M

.SYSTEM COMMAND: ls *.OMM (e.g.)
[Enter the command you want executed. This may also be a command file.
Substitution of do-loop indices and register contents for characters within {} is allowed anywhere in the command line (not just in filenames). In addition it is now possible to substitute register contents in floating point format, see NOTE: 5 below]

NOTES

1. Comments are not accepted in the command line as a SPIDER comment character (;) is used to string system commands together on the same line in Unix.

2. For 'VM M' multiline input is accepted until a line has only a intial '.' (dot). To put a blank at the end of a line, place it at the beginning of the following line or it will disappear.

3. You must specify the extension for any filenames within the system command as they are NOT appended automatically by SPIDER (as there is no way to recognize what is a filename). However, you can use the string: $DATEXT to substitute the current SPIDER data extension into the corresponding position in your command line. You can use the string: $PRJEXT to substitute the current SPIDER project extension into the corresponding position in your command line.

4. The "VM" name for this operation is left over from the VAX/VMS system operation name.

5. Sample of substituting register contents in floating point format:

   x11=34.56

   VM ; To write out the following: x11 is now= 34.5600
   echo x11 is now= {%F7.4%x11}

   VM ; To write out the following: x11 is now= 3.4560E+01
   echo x11 is now= {%ES11.4%x11}

   Place the FORTRAN format within '%' symbols followed by the register whose contents are to be substituted. All of this has to be enclosed within the wavy brackets.

6. Samples of usage within SPIDER loops (on Unix).

    
         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 
         -- sample loop for converting series of 1024 x 512 raw images  
         -- to SGI rgb format
    
         X11 = 1024     ; nsam 
         X12 = 512      ; nrow 
         DO LB1 I=1,1   ; loop 
         VM             ; use "imgcopy" to convert images 
         frombin raw{***i}.$DATEXT   sgi{***i}.rgb {****x11} {***X12}  
         LB1            ; end loop 
         
    
         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    
         --sample loop for renaming/renumbering series of SPIDER images 
    
         X33=33  
         DO LB2 I=1,4     ; loop 
         VM               ; system call for renumbering 
         cp jnk{***X33}.vms    jnk444{***I}.vms  
         X33=X33+1 
         LB2              ; end loop 
         
    
         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    
         --sample loop for consecutively renaming/renumbering series of SPIDER  
         -- while skipping any missing image numbers 
    
         X11=0                ; initialize output file number counter 
         DO LB3 I=1,4         ; loop 
         FI N                 ; use "FI N" to see if file exists 
         jnk{***I}            ; filename 
         IF(X2.LE.0)GOTO LB3  ; skip if file not found 
         X11=X11+1            ; increment output file number counter 
         VM                   ; system call for renaming/renumbering SPIDER images 
         cp jnk{***I}.vms   jnk444{***X11}.vms  
         LB3                  ; end loop 
         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    
         --Sample showing symbolic parameter substitution within 
           a procedure 
    
           X11=55            ; set register 11 outside of procedure   
                             ; (binding time for parameter substitution is 
                             ;  before procedure is executed!) 
           @testvm           ; invoke <I>testvm</I> SPIDER procedure 
           doc               ; value given to FILENAME PATTERN solicited 
                             ; in <I>testvm</I> procedure 
         Contents of invoked procedure <I>testvm</I>: 
               FR                              
               ?ENTER FILENAME PATTERN?<1>     
               VM                             
               rm <1>{***X11}.$DATEXT  
         Result of invoked procedure: 
               rm doc055.DAT 
         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    
         

SUBROUTINES

VMS

CALLER

DRIV1