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[ccp4bb]: Water molecule environment - summary



Dear all,

Thank you very much for all the answers sent through the ccp4bb or directly to me. My question was :
I am working on the refinement of a crystal structure at 2.9-A resolution. I have been adding a few water molecules and would like to find a utility which could give me a list of the residues which are (probably) hydrogen-bonded to each of the water molecules.
I was told that there was a software by B. Hazes that could do this but did not succeed in finding it.
Thank you very much in advance,

Your answers were :
- CONTACT (!!!) and WATERTIDY
from the CCP4 suite (Contact was exactly the tool I wanted, except that it does not always give the chain IDs of the water molecules - which are distributed between different chains in my PDB file)
- HBplus : http://www.biochem.ucl.ac.uk/~mcdonald/hbplus/home.html
- WAP : http://144.16.71.11/wap (actually I had several problems loading my PDB to this online tool)
- LIGPLOT : http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html
- SMS : http://www.cbi.cnptia.embrapa.br
- WhatIF (?) : http://www.cmbi.kun.nl/gv/servers/WIWWWI/

and...

- MCFMAN : http://eagle.mmid.med.ualberta.ca/highlights.html
Here follows the details from Bart HAZES
The program referred to above is called MCFMAN (MCF being the Univ. of Groningen PDB-format derivative) and it is a bunch of tools to manipulate MCF or PDB files, just like PDBMAN and others. Given the protein coordinates and (potential) water coordinates in separate files the program will do a sanity check on each water. The user can specify if a water must make a hydrogen bond with at least one protein atom within a user-specified distance, it also checks for steric clashes (BMP), no close interactions with protein at all (FAR), or positions very close to a purely rotational symmetry axis (this gives steric clashes between symmetry related waters). In the later case the program can put the water exactly on top of the symmetry axis for you (that's what XPLOR/CNS want). All potential water positions are transformed by symmetry to be as close to the protein as possible.

If you wish you can pick up the program from http://eagle.mmid.med.ualberta.ca/highlights.html
It should compile with a standard Fortran 77 compiler without needs for any external libraries.

The commands of interest are GETPDB to read in the protein coordinates, WATPEK to read the water coordinates and do the analysis, and MAKPDB to make a new PDB with the water positions added. Documentation for these
and all other commands can be looked at by typing COMMAND HELP or by
looking at the top of the source code file.

Thank you once more,

Loïc


-----------------------
Loic BERTRAND, PhD
Department of Biochemistry - Sanger building
University of Cambridge
80 Tennis Court Road
CB2 1GA Cambridge - England