Re: [ccp4bb]: Link to symmetry related atom in Refmac5

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Dr Nicholas Keep wrote:
> 
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> 
> Does anyone know how you explicitly specify a link to a symmetry related
> atom in refmac5.
> I request symmetry related links in the GUI and have checked the COM
> file is giving the option I expect.


 You need to use the full PDB format for LINKS with a REFMAC extension
if you need it:


Here are my CA links - the symmetry number is defined as 
nsym ( here 1)
origin shift ( here 0 0 0 ) ie symmetry X,Y,Z
LINK     1   OE1 GLU A 278                CA   IUM W   1     1555   1555
LINK     1   OD1 ASP A 307                CA   IUM W   1     1555   1555
LINK     1   OE1 GLU B 276                CA   IUM X   1     1555   1555
LINK     1   O   HOH R  33                CA   IUM W   1     1555   1555
LINK     1   O   HOH R  40     2.60       CA   IUM W   1     1555   1555



LINK     1   OE1 GLU A 276                CA   IUM W   1     1555   2645

would indicate that OE1 GLU 278 A was linked to CA 1 W via
 the second sym op with origin shift (1,-1,0)

The sym op order comes from that in $CLIBD/symop.lib

If you use the CHECK NONE option then REFMAC5 only uses your defined
links,
CISPEPs Disulphides etc..

The library file looked like this.. Not sure what it did about the HOH
CA links 
You can assign the length you need but not the SD which makes it a bit
problematic
for CA and I cant find the format off hand in the document.


global_
_lib_name         mon_lib
_lib_version      3.0
_lib_update       31/05/00
#
# ---   LIST OF LINKS ---
#
data_link_list
loop_
_chem_link.id
_chem_link.comp_id_1
_chem_link.mod_id_1
_chem_link.group_comp_1
_chem_link.comp_id_2
_chem_link.mod_id_2
_chem_link.group_comp_2
_chem_link.name
GLU-CA   GLU      .        .        CA       .        .
 bond_GLU-OE1_=_CA-CA
GLU-CA1  GLU      .        .        CA       .        .
 bond_GLU-OE2_=_CA-CA
ASP-CA   ASP      .        .        CA       .        .
 bond_ASP-OD2_=_CA-CA
ARG-ARG  ARG      .        .        ARG      .        .
 bond_ARG-NH2_=_ARG-NH2
symmetry GLU      .        .        CA       .        .
 bond_GLU-OE1_=_CA-CA
symmetry GLU      .        .        CA       .        .
 bond_GLU-OE2_=_CA-CA
symmetry ASP      .        .        CA       .        .
 bond_ASP-OD2_=_CA-CA
# ------------------------------------------------------
#
# --- DESCRIPTION OF LINKS ---
#
data_link_GLU-CA
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
 GLU-CA   1 OE1   2 CA      .           2.320    0.020
#
data_link_GLU-CA1
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
 GLU-CA1  1 OE2   2 CA      .           2.320    0.020
#
data_link_ASP-CA
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
 ASP-CA   1 OD2   2 CA      .           2.320    0.020
#
data_link_ARG-ARG
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
 ARG-ARG  1 NH2   2 NH2     .           1.400    0.020
# ------------------------------------------------------