*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
We have a covalently modified amino acid side chain. We're trying to
generate a link for REFMAC refinement, but failing so far. Wit's end
is within sight. Any suggestions?
Thanks,
Pat
------------------------------------------------------------------------
-----------------------------
THIS IS THE ERROR:
FORMATTED OLD file opened on unit 45
Logical name: ATOMSF, Filename:
/usr/local/programs/CCP4/ccp4-5.0.2/lib/data/atomsf.lib
ERR: item _chem_link_bond.link_id :DS not found in the list of
links
BLOCK :data_link_DS
************************************************************************
***
* Information from CCP4Interface script
************************************************************************
***
The program run with command: refmac5 XYZIN etc. etc. etc
has failed with error message
Floating Exception
------------------------------------------------------------------------
-----------------------------
THIS IS WHAT WE HAVE AT THE END OF OUR LIBRARY FILE:
# --- LIST OF LINKS ---
data_link_list
loop_
_chem_link.id
_chem_link.name
_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
DS AttachD-S DRG . . SER . .
#
# --- DESCRIPTION OF LINKS ---
#
data_link_DS
#
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
DS 1 CAA 2 OG single 1.450 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
DS 1 CIA 1 CAA 2 OG 109.500 3.000
DS 1 CAA 2 OG 2 CB 109.500 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
DS co 1 CIA 1 CAA 2 OG 2 CB 90.00 10.0 2
#
# ---------------
------------------------------------------------------------------------
---------------
Patrick J. Loll, Ph. D. (215) 762-7706
Associate Professor FAX: (215) 762-4452
Department of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
[EMAIL PROTECTED]
