CONTACT computes inter or/and intra molecular contacts;
* can compute contacts only for special atoms ( for example
for potential H-bonds);
* can generate additional symmetry related atoms (with
occupancy = 0) which are closed to initial molecule;
can do it only for water molecules (water structure);
* checks atoms in special positions and changes multiplicity
for these atoms.
Author: A.A.Vagin
email: alexei@ysbl.york.ac.uk
Reference:
A. A. Vagin, G. N. Murshudov and B. V. Strokopytov
BLANC: the program suite for protein crystallography
J. Appl. Cryst. (1998). 31, 98 - 102
Copy file contact.tar.gz
and uncompress it (`gunzip contact.tar.gz')
After untaring `contact.tar' , you will get a contact directory,
with src and bin subdirectories. To build the executable,
go in src and then you have to option
1. `make all', the executable (contact) will finish up in the bin
directory; providing the full pathname (.../contact/bin/contact) one
can execute it from anywhere without having to define and environmental
variable.
2. `make all_ln` Linux distribution
It is easy to use CONTACT interactively, but can be used in batch.
To get started with CONTACT interactively, you first have to answer two questions:
1. Do you want to have FILE-DOCUMENT ("contact.doc") ? /<N>/Y/:
and
2. input-PDB_file :
Next you can use keywords if you like
The available keywords are:
CUT: <3.5> - distance cut_off.
DLIM: <0.5> - minimal distance to recognize atom in special position.
if dist (betweem symmetry related atoms) < DLIM then
atom is in special position.
MOD: <S>/I/B/N: S - intra molecular contacts.
I - inter molecular contacts.
B - both molecular contacts.
N - generate symmetry related atoms around initial molecule
and add its to output file (see alse WAT="S").
if MOD="N" and WAT="S" program set WAT="Y."
HBOND: <N>/Y : Y - only potential H-bond contacts ( just contacts between:
O - O , O - N and N - N atoms).
WAT: <N>/Y/S : N - without water, Y - with, S - only water structure -
generate symmetry related water molecules around initial
molecule and add its to output file.
SPEC: <N>/Y : Y - special contacts between TYPE1 and TYPE2.
TYPE1 < > - type of atom_1, for example "S" means all sulfur atoms.
TYPE2 < > - type of atom_2, " " means all atoms.
FILE_O: < > - output PDB_file of coordinates, " " means without this
file.