MSA        Run multivariate statistical analysis  

 

file format: SPIDER

SEE ALSO:  msaimc2doc, msamap, msavismap


USAGE:    msa

          .Input file example: image001
          [Enter the name of the image or volume containing densities]

          .Use number string:N, or document file:D : N
          
           If N was answered:
 
               .File numbers: 1-100,210-200,401-10000 
             [Enter string that describes file numbers. Program cannot handle 
              missing files (the old coran in SPIDER 5.0 could do this). So, if
              you have gaps, which is common, use the document file option. ]
          
           If D was answered:
   
                 Document file name with file numbers: Filelistdoc001
              [Enter the name of a document file that has the file numbers or a 0/1 
               selection file. Both should work, see question below.]
           
              Column number to use (0 = use as 0/1 selection file): 3
              [Enter the column number that contains the file number. If 0
              is entered then the program uses column 1 as a 0/1 indicating if 
              the file is to be used, and the key column as file number.]
           
           .Mask file: mask001
           [Enter the name of the file containing the image binary image mask.
            Only the pixels in the image that coinside with the 1s in the mask
            are used for MSA analysis.]
            
           .Number of factors: 8
           [Enter the number of factors (eigenvectors) to be calculated.]
           
           .Run CORAN (def.), or PCA: Coran
           [Enter which type of analysis to run. Only the first letter is
           used, but the answer may be longer.]
           
           .Additive constant: 1.
           [Enter an additive constant so that for correspondence analysis
           there are no negative vlaues in the data.]
           
           .Prefix for output files: molecule
           [Enter a prefic that is used to construct several file names. These
           are: _IMC., _PIX., and _EIG..
           Unfortunately these file names do not comply with spider file 
           naming conventions. However, later programs need them also with 
           this type of names. (this program was extracted from spider).

Notes:    The program was extracted from spider. 

Programs: em_msa.py, jpmsk1.f and subrountines

Author(s): M. Radermacher: for .py and rewrite of jpmsk1 for stanalone, 
           J.P. Bretaudier for the original JPMSK1 and subroutines, and
           members of the Albany lab for the rewrite of a large part of the
           code.