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Garib
On 7 Dec 2005, at 13:14, Masaki UNNO wrote:
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Dear all
My question is similar to what many people have asked before but a
little
different.
I am refining a structure which contains a porphyrin-like compound
(but not
a heme). The compound contains an iron, which seems to be coordinated
by
His. The distance between iron and His NE2 is around 2A judged by
electron
density map. However, after refmac5 refinment, the distance is always
around 2.5A. (Electron density map shows a little strange CA-CB-CG
angle in
His) So, I want to include the restraint between iron and His NE2.
So I created an extra library file. However, refmac5 do not complete
with
error message:
ERR: item _chem_link_bond.link_id :DRG-HIS not found in the list
of
links
BLOCK :data_link_DRG-HIS
I visited the following URL
http://www.ysbl.york.ac.uk/~alexei/dictionary.html#example_link
and found FE-CYS in "_data_link.id" but not FE-HIS.
What should I change the extra libraly which is wirtten as follows ?
DRG is
a tentative name of my compound.
Best regards.
# --- 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
DRG-HIS DRG . . HIS . . bond_DRG-HIS
data_link_DRG-HIS
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
DRG-HIS 1 FE 2 NE2 single 1.855 0.020
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
DRG-HIS 1 ND 1 FE 2 NE2 110.000 3.000
DRG-HIS 1 FE 2 NE2 2 CD2 120.000 3.000
loop_
_chem_link_tor.link_id
_chem_link_tor.id
_chem_link_tor.atom_1_comp_id
_chem_link_tor.atom_id_1
_chem_link_tor.atom_2_comp_id
_chem_link_tor.atom_id_2
_chem_link_tor.atom_3_comp_id
_chem_link_tor.atom_id_3
_chem_link_tor.atom_4_comp_id
_chem_link_tor.atom_id_4
_chem_link_tor.value_angle
_chem_link_tor.value_angle_esd
_chem_link_tor.period
DRG-HIS ih 1 NA 1 FE 2 NE2 2CE1 180.000 10.000
==========================
Masaki UNNO Ph.D.
Institute of Multidisciplinary Research
for Material
Tohoku University
tel +81-22-217-5117 or
+81-22-217-5749
fax +81-22-217-5118
========================
