The Ramachandran plot in Coot is not based on PROCHECK, it never was!!! It is based on the molprobity one, however it needs updating and currently not based on the latest distribution (*).
B (*) a Clipper/Kevin thing for the interested... > Paul, is it planned to replace the Ramachandran check based on PROCHECK with > one based on MOLPROBITY? At least in v. 0.7 for Mountain Lion it was > still not available.... > Best, > Xavier > > > On 25/3/13 5:33 PM, Paul Emsley wrote: >> On Wed, 2013-03-20 at 13:24 +0000, Anat Bashan wrote: >>> Hi All, >>> >>> I build a ligand that is partly RNA and Partly a protein chain. In between >>> I have a special nucleotide with a N bound to C3' (instead of O3'). it is : >>> CC-PPU-Ala-Phe-Val. I have links in the .pdb file and the PPU is a known >>> ligand to COOT. My links connect the N3' of the PPU with the C of Ala. >>> nevertheless, if I try to regularize or refine the Ala keeps moving away >>> from the PPU. The other link I defined between the C and the PPU works fine. >>> What am I missing here ? >>> Do I need to specify anything else than the LINK? >>> I attached the .pdb file of my ligand for you to be able to load into coot >>> and try playing with it yourself. >> Sorry for the delay (I was a bit disconnected and distracted at the CCP4 >> dev meeting). >> >> So, what you are missing, it seems to me, is the use of JLigand (that's >> the best tool AFAIK) to define the link between the Ala and the PPU. >> This link is not in the refmac monomer library and you have to tell Coot >> (and Refmac) exactly what you mean (libcheck helps out). >> >> You do not need to explicitly make the link, Coot will do that for you >> as you use JLigand. >> >> HTH, >> >> Paul. >> > > -- -- *************************************************** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
