The reminiscence to the procheck plot comes from the default 10 degree block size in Coot rather than using a smooth curve as in molprobity. But you can change this if you like. It wont change your outliers though (*) ;-) . See:
http://www.biop.ox.ac.uk/coot/doc/coot/Ramachandran-Plots.html B (*) but may be a bit slower... > Ok, sorry for that...it was just that the picture of the Ramachandran, > with the allowed and disallowed regions, reminds > strongly of the one in PROCHECK. It actually does not look like the > one from MOLPROBITY (see attachments). > > > On 4/4/13 9:18 PM, Bernhard Lohkamp wrote: >> 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
