Those error messages are warnings - not fatal errors - there must be something else reported in the log file to cause that.
But as Garib says DNA "standard" names vary according to program and year - see if your atom names are those in the $CLIBD/monomers/g/GUA.cif That is where REFMAC will find its default dictionary. Eleanor On 15 May 2012 16:56, Garib N Murshudov <[email protected]> wrote: > Dear Vidisha > > The easiest way is to convert DNA names to standard pdb v3 names. You can > do it using molprobity. The probelem is that GUA may have different meaning > than G (RNA) or DG (DNA). > > regards > Garib > > On 15 May 2012, at 16:37, tipu Lall wrote: > > Dear CCP4 users, > > > I am a beginner in this field. It would be kind of all of you if can help > me how to move ahead with my problem. > > > I have an output file from CNS of a binary complex (DNA-protein) and I am > trying to refine it with refmac5 (restrain refinement) and job is failing > with error messages (written below) > > > Before restrain refinement, I converted the CNS output file (pdb) from > Codconv of CCP4 to pdb format. > > > Thanks in advance > Vidisha > > > INFO: link is found (not be used) dist= 3.003 ideal_dist= 2.400 > ch:CC res: 1 GUA at:C2' .->ch:Ca res: 2 GUA > at:O2P . > INFO: link is found (not be used) dist= 2.625 ideal_dist= 2.400 > ch:CC res: 1 GUA at:C3' .->ch:Ca res: 2 GUA > at:P . > INFO: link is found (not be used) dist= 2.797 ideal_dist= 2.400 > ch:CC res: 1 GUA at:C3' .->ch:Ca res: 2 GUA > at:O2P . > INFO: link is found (not be used) dist= 1.606 ideal_dist= 2.400 > ch:CC res: 1 GUA at:O3' .->ch:Ca res: 2 GUA > at:P . > INFO: link is found (not be used) dist= 2.499 ideal_dist= 2.400 > ch:CC res: 1 GUA at:O3' .->ch:Ca res: 2 GUA > at:O1P . > INFO: link is found (not be used) dist= 2.504 ideal_dist= 2.400 > ch:CC res: 1 GUA at:O3' .->ch:Ca res: 2 GUA > at:O2P . > INFO: link is found (not be used) dist= 2.507 ideal_dist= 2.400 > ch:CC res: 1 GUA at:O3' .->ch:Ca res: 2 GUA > at:O5' . > INFO: link is found (not be used) dist= 2.843 ideal_dist= 2.400 > ch:CC res: 1 GUA at:O3' .->ch:Ca res: 2 GUA > at:C5' . > INFO: link is found (not be used) dist= 2.637 ideal_dist= 2.400 > ch:Ca res: 2 GUA at:C3' .->ch:Cb res: 3 ADE > at:P . > INFO: link is found (not be used) dist= 3.116 ideal_dist= 2.400 > ch:Ca res: 2 GUA at:C3' .->ch:Cb res: 3 ADE > at:O1P . > INFO: link is found (not be used) dist= 1.604 ideal_dist= 2.400 > ch:Ca res: 2 GUA at:O3' .->ch:Cb res: 3 ADE > at:P . > INFO: link is found (not be used) dist= 2.504 ideal_dist= 2.400 > ch:Ca res: 2 GUA at:O3' .->ch:Cb res: 3 ADE > at:O1P . > INFO: link is found (not be used) dist= 2.514 ideal_dist= 2.400 > ch:Ca res: 2 GUA at:O3' .->ch:Cb res: 3 ADE > at:O2P . > > > ATTENTION: atom:O4 GUA 1 CC is missing in the structure > ATTENTION: atom:O3 GUA 1 CC is missing in the structure > ATTENTION: atom:C3 GUA 1 CC is missing in the structure > ATTENTION: atom:C1 GUA 1 CC is missing in the structure > ATTENTION: atom:O1 GUA 1 CC is missing in the structure > ATTENTION: atom:O2 GUA 1 CC is missing in the structure > > > ===> Error: Fatal error. Cannot continue > > > > > Dr Garib N Murshudov > Group Leader, MRC Laboratory of Molecular Biology > Hills Road > Cambridge > CB2 0QH UK > Email: [email protected] <[email protected]> > Web http://www.mrc-lmb.cam.ac.uk > > > > >
