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
