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-scale spacial sky gradients might still be present and can 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? (split = no) Use split images during processing? (merge = no) Merge amplifiers from same CCD? (xtalkfile = "!xtalkfil") Crosstalk file (fixfile = "BPM") List of bad pixel masks (saturation = "!saturate") Saturated pixel threshold (sgrow = 1) Saturated pixel grow radius (bleed = "20000.") Bleed pixel threshold (btrail = 15) Bleed trail minimum length (bgrow = 1) Bleed pixel grow radius (biassec = "!biassec") Overscan strip image section (trimsec = "!trimsec") Trim data section (zero = "Zero") List of zero level calibration images (dark = "Dark") List of dark count calibration images (flat = "Flat*") List of flat field images (sflat = "Sflat990327V3I.fits") List of secondary flat field images (minreplace = 1.) Minimum flat field value\n (interactive = no) Fit overscan interactively? (function = "minmax") Fitting function (order = 1) Number of polynomial terms or spline pieces (sample = "*") Sample points to fit (naverage = 1) Number of sample points to combine (niterate = 1) Number of rejection iterations (low_reject = 3.) Low sigma rejection factor (high_reject = 3.) High sigma rejection factor (grow = 0.) Rejection growing radius (fd = "") (fd2 = "") (mode = "ql")Throughout the reduction process, but particularly at this step, it would be wise to visually inspect all the images to make sure that you are actually improving things!