Dear Dr. Murshudov,
I am working on the heme protein with a surface Cys residue
covalenlty linked to another molecule through its SG atom.
Here is a part of log file.
------------------
INFO: link is found (not be used) dist= 2.188 ideal_dist=
2.300
ch:AA res: 400 CYS at:SG .->ch:Aa res: 500
HEM at:FE .
INFO: link is found (not be used) dist= 2.316 ideal_dist=
2.300
ch:BB res: 400 CYS at:SG .->ch:Ba res: 500
HEM at:FE .
INFO: link is found (not be used) dist= 2.398 ideal_dist=
1.610
ch:BB res: 97 CYS at:SG .->ch:Bb res: 501
R7A at:C49 .
-------------------
How can I turn on only the third link? I am using the refmac5.5.0102
on ccp4i.
If I choose the link option "residues are close only" for non-
standard monomers (under "setup geometric restraints" menu), I see
the following messages but the refinement stops.
--------------------
$TEXT:Warning: $$ Potential and actual links $$
WARNING : link:CYS-HEM is found dist = 2.184 ideal_dist=
2.300
ch:AA res: 400 CYS at:SG .->Aa res: 500
HEM at:FE .
$$
$TEXT:Warning: $$ Potential and actual links $$
WARNING : link:CYS-HEM is found dist = 2.315 ideal_dist=
2.300
ch:BB res: 400 CYS at:SG .->Ba res: 500
HEM at:FE .
$$
$TEXT:Warning: $$ Potential and actual links $$
WARNING : description of link:CYS-R7A is not in the dictionary.
link will be created with bond_lenth = 1.610
$$
$TEXT:Warning: $$ Potential and actual links $$
WARNING : link:CYS-R7A is found dist = 2.404 ideal_dist=
1.610
ch:BB res: 97 CYS at:SG .->Bb res: 501
R7A at:C49 .
If you are happy with the library description then use the keyword
(MAKE CHECK NONE)
I.e. do not check correctness of the coordinates
===> Error: New ligand has been encountered. Stopping now
Refmac_5.5.0102: New ligand has been encountered. Stopping now
------------------
I will appreciate solutions.
Young-Tae
