Easiest way is to line up molecule pairs or chain pairs in COOT and see if there are equivalent waters.
If the number of waters is too large to inspect manually, save the superposed structures to disk, grep out the waters from each into a separate files, and use a program like http://www.cytbc1.com/berry/for/pdbdist3w.for to compare files and write atoms closer than a specified threshold into a new pdb file That program only compares two files, so you would have to do all possible pairs to get waters conserved in at least 2 structures, or compare each file with the survivors from previous to get waters conserved in all. PS- It compiles with f77 (g77). May need touch-up for fortran90 (gfortran). eab On 06/07/2017 02:59 AM, Eleanor Dodson wrote:
Many years ago I wrote code to label waters with a code related to the residue/atom they were Hbonded to , so then you could check whether all OH TYR 227 in each chain had an associated water.. But it used non-standard water naming .. Easiest way is to line up molecule pairs or chain pairs in COOT and see if there are equivalent waters. Eleanor On 7 June 2017 at 00:30, gerardo andres <0000130afa955101-dmarc-requ...@jiscmail.ac.uk <mailto:0000130afa955101-dmarc-requ...@jiscmail.ac.uk>> wrote: Hi everyone, does anyone know any strategy or program (besides pywater) to identify conserved waters in a protein? Thanks, Gerardo
