In your run with the option "residues are close only" refmac also
should generate a pdb file with link records added. In very simple
form you can edit this pdb file and remove all unnecessary links and
leave link you want. Then you can rerun with normal options and
generated library.
Better option is to create links carefully with bond, anlges,
chrialities etc. It can be done (I am repeating myself) using JLigand
from:
http://www.ysbl.york.ac.uk/mxstat/JLigand/1.html
the second tutorial in this site is how can create and use covalent
links (hopefully at some point it will be done via coot).
If any question or problem please let me know and I will try to sort
it out.
regards
Garib
On 25 Jun 2010, at 00:42, Young-Tae Lee wrote:
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
