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Hello colleagues Thanks for all the suggestions which are indeed helpful, especially the Molprobity way dealing with the issue. Chen, thanks for the video which is informative. In fact in my case Refmac was still able to refine other parts of the structure and terminate normally but when we looked into the log file it caught our attention that some items in the RNA chain were indeed missing: ATTENTION: atom:OP3 U 1 DD is missing in the structure ATTENTION: atom:O5' C 3 DD is missing in the structure ATTENTION: atom:C5' C 3 DD is missing in the structure ATTENTION: atom:C4' C 3 DD is missing in the structure ATTENTION: atom:C3' C 3 DD is missing in the structure ATTENTION: atom:O3' C 3 DD is missing in the structure ATTENTION: atom:C2' C 3 DD is missing in the structure ATTENTION: atom:O2' C 3 DD is missing in the structure ATTENTION: atom:C1' C 3 DD is missing in the structure ATTENTION: atom:O4' C 3 DD is missing in the structure ATTENTION: atom:N1 C 3 DD is missing in the structure ATTENTION: atom:C6 C 3 DD is missing in the structure ATTENTION: atom:C5 C 3 DD is missing in the structure ATTENTION: atom:C4 C 3 DD is missing in the structure ATTENTION: atom:N4 C 3 DD is missing in the structure ATTENTION: atom:N3 C 3 DD is missing in the structure ATTENTION: atom:C2 C 3 DD is missing in the structure ATTENTION: atom:O2 C 3 DD is missing in the structure Frankly we would not have been aware of this if we didn't go into the log file. Sam On 26 April 2016 at 21:33, Chen Zhao <[log in to unmask]> wrote: > Hi Sam, > > If you haven't, you could watch this video on how to use RCrane: > https://www.youtube.com/watch?v=ZsqAd-BVU50 > > I myself just used it very briefly before and encountered no problem with > Refmac. I asked my lab member who built a 20 nt RNA structure with it and > encountered no problem with Refmac either. > > Good luck, > Chen > > On Tue, Apr 26, 2016 at 8:28 AM, Francis Reyes <[log in to unmask] > > wrote: > >> Hi Sam >> >> As someone who's built nucleic acids for a long time, I understand the >> frustration with the RNA nomenclature. >> >> May I suggest using the pdb remediator from the Richardson group >> (available at >> https://urldefense.proofpoint.com/v2/url?u=http-3A__kinemage.biochem.duke.edu_software_remediator.php&d=AwIFAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=gSXo4C8rqJ9XkrmffW_ue3fdnKcxQ2XBorlZY7APB2A&s=FbYgBE5kA9O2lUoILoZbegODn3aAN9SY0U6C4MuXQ6U&e= >> ) ? >> >> The 'new' (versus using --old) works quite well with coot and RCrane. >> >> F >> >> >> On Apr 22, 2016, at 2:16 AM, Sam Tang <[log in to unmask]> wrote: >> >> > Hi again >> > >> > I am wondering if anyone has the experience using a plugin in Coot >> called RCrane to build RNA and then refine with Refmac. It happens that >> refmac cannot recognize my di-/tri-nucleotide and complains of missing >> atoms. No problem for single nucleotides built from the Coot library. >> > >> > Would be glad if anyone with similar experience could share further on >> this. >> > >> > Thanks in advance. >> > >> > Kind regards >> > >> > Sam >> > >> > Biochemistry Programme, School of Life Sciences, CUHK >> > >