I should maybe add some code to orthonormalise the matrix if it's not too far off (which would be approximate). I haven't looked at this program for a long time (nor indeed used it), so don't hold your breath
Phil On 1 Apr 2015, at 22:52, Shane Caldwell <shane.caldwel...@gmail.com> wrote: > Hi ccp4bb, > > I'm trying to solve a problem I never quite figured out in the past. I'd like > to use the sortwater utility to send my picked waters to various protein > chains, and to give them the same residue number if they are NCS-equivalent, > as the manual outlines. > > http://www.ccp4.ac.uk/html/sortwater.html > > The first part goes off perfectly, partitioning the waters into their > respective chains. Where I run into problems is bringing in NCS. I can't get > the program to recognize the transformation matrix. I can calculate the > matrix using superpose, and manually input these (limited precision) values > into my script, which looks like: > > NCS B C MATRIX 0.072 0.997 -0.012 0.991 -0.073 -0.113 -0.113 -0.004 -0.994 > 37.502 -35.283 81.276 > > and it returns > > WARNING: **** Matrix is not orthonormal **** > > > My linear algebra is very limited, and I don't know exactly what this means > in the context of this program, though I suspect it could be either linked to > converting to fractional coordinates (I'm in a monoclinic system), or a > product of the limited precision of the matrix values. > > Using the identity matrix, like so: > > NCS B C MATRIX 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 > 0.00000 1.00000 0.000 0.000 0.000 > > doesn't trigger the warning. These values have more digits, but adding extra > zeroes to the original matrix as a very crude workaround still returns the > error. > > So, I'm now stuck trying to parse what's going on. I know sortwater also > takes O datablocks as matrix input, and that's something I could look into > (especially if calculating in a different program might get me better > precision). Although, I'm not sure the format is a factor given the identity > matrix is accepted as a keyword input. > > Skimming the archives, I get the sense this isn't something that many users > do any more. I have quite a few structures with hundreds of waters each and > I'd like to get the waters organized, but doing it by hand will take a very > long time. Any help getting this program running would be greatly appreciated! > > > Shane Caldwell > McGill University
