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If you are having similar problems, this should not be happening but
this is Garib's answer:
If you are using ccp4i then you should switch "sugar-sugar and
sugar-peptide if" to "defined in file only"
That is under "Setup Geometric Restraints"
This works,
Jan
=================================================================
This was my original question:
Refmac5 keeps creating and to my suspicion USING links between an ion
and sugar even if
I use 'make LINKS N' and when I remove the links from the .pdb and the
created .cif files
Refmac stops as it 'finds new ligand' and I should go and check the
library.
Any other methods I can avoid Refmac5 creating those links?
Jan
Bits of Refmac output:
//////////////////////////////////
Data line--- make check NONE
Data line--- make hydrogen YES hout NO peptide NO
cispeptide YES ssbridge YES symmetry YES sugar YES
connectivity NO * link NO*
Data line--- refi type REST resi MLKF meth CGMAT bref ISOT
Data line--- ncyc 10
Data line--- scal type SIMP reso 2.102 137.361 LSSC
ANISO EXPE
Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
Data line--- weight MATRIX 0.3
Data line--- monitor MEDIUM torsion 10.0 distance 10.0 angle
10.0 plane 10.0 chiral 10.0 bfactor 10.0 bsphere
10.0 rbond 10.0 ncsr 10.0
Data line--- labin FP=F_run3__run4 SIGFP=SIGF_run3__run4
FREE=FreeR_flag
Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT
PHDELWT=PHDELWT FOM=FOM
////////////////////////////////////
*WARNING : description of link:GAL-NA not found in the dictionary.
link will be created with bond_lenth = 2.240
WARNING : link:GAL-NA is found dist = 2.247 ideal_dist= 2.240
ch:Ga res: 2 GAL at:O6 .->Na res: 2 NA
at:NA .
WARNING : link:GAL-NA is found dist = 2.250 ideal_dist= 2.240
ch:Ge res: 6 GAL at:O6 .->Ne res: 6 NA
at:NA .*
////////////////////////////////////
This is from the current Refmac manual:
N - check links between residues and *give information about them in the
log file, but do not use them UNLESS they are specified by record LINK
in the input coordinate file*.
--------------------------------------------------
At the moment there are no LINKS records in the input pdb file.
