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: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
