To apply your new sky-flat to your object frames requires that you run ccdproc again, this time with only the sky flat option turned on. By turning the other options off you save a little bit of time per image as ccdproc would otherwise check the header of every CCD image to make sure the other reduction steps had been performed. We generally test the result of applying our sky-flat on a few images before applying the flat to an entire data set. Slight large spatial scale sky gradients might still be present and can will be removed later with mscskysub, however, if the sky-flat is helping the resulting images should not have any patchy or chip by chip residuals.

PACKAGE = mscred
   TASK = ccdproc

images  = @objectstosflat.list  List of Mosaic CCD images to process
(output = @objectsflatout.list) List of output processed images
(bpmasks=                     ) List of output bad pixel masks
(ccdtype=               object) CCD image type to process
(noproc =                   no) List processing steps only?

(xtalkco=                   no) Apply crosstalk correction?
(oversca=                   no) Apply overscan strip correction?
(trim   =                   no) Trim the image?
(fixpix =                   no) Apply bad pixel mask correction?
(zerocor=                   no) Apply zero level correction?
(darkcor=                   no) Apply dark count correction?
(flatcor=                   no) Apply flat field correction?
(sflatco=                  yes) Apply sky flat field correction?
(merge  =                   no) Merge amplifiers from same CCD?

(saturat=                INDEF) Saturation (+val=e-, -val=ADU)
(xtalkfi=                     ) Crosstalk file
(biassec=                     ) Overscan strip image section
(trimsec=                     ) Trim data section
(fixfile=                     ) List of bad pixel masks
(zero   =                     ) List of zero level calibration images
(dark   =                     ) List of dark count calibration images
(flat   =                     ) List of flat field images
(sflat  =  Sflat990327V3I.fits) List of secondary flat fi
(minrepl=                   1.) Minimum flat field value

(interac=                   no) Fit overscan interactively?
(functio=               minmax) Fitting function
(order  =                    1) Number of polynomial terms or spline pieces
(sample =                    *) Sample points to fit
(naverag=                    1) Number of sample points to combine
(niterat=                    1) Number of rejection iterations
(low_rej=                   3.) Low sigma rejection factor
(high_re=                   3.) High sigma rejection factor
(grow   =                   0.) Rejection growing radius
(fd     =                     )
(fd2    =                     )
(mode   =                   ql)