Re: [COOT] Updating maps

Dear Murpholino, The problem is the auto open MTZ. In your case the —auto option does not assign F and SIGF. You need to use "open mtz" and assign them using the option menu and the Rfree as well. Regards, Lucrezia Sent from Outlook for iOS __

Re: [COOT] How does COOT determine protonation states

Dear Kate, Coot adds hydrogen atoms according to the dictionary. If you want to change the protonation of a ligand, you'd do that by modifying the actual monomer dictionary. We typically use Acedrg to generate dictionaries. For example, in the case of a ASP residue, the modification which descri

Re: [COOT] N-acetyl methionine

Dear Clemens, The AME component is ‘non-polymer’. Therefore, you need to create a link between your residue and AME. For example, if your residue type is ALA, the instruction file for generating the link in AceDRG will be: LINK: RES-NAME-1 ALA ATOM-NAME-1 C RES-NAME-2 AME ATOM-NAME-2 N BOND-TYPE

Re: [COOT] MDO Unnatural modified Amino acid

Hi Kelvin, I tried the following on 7tqr, and it seems to work. I am using coot 0.9.8.92 (CCP4): Get monomer MDO merge MDO in the model and fit into the density MDO now has number 617, this needs to be changed to 141. Edit renumber residue: select the model, and then ‘Start Residue’ 617, ‘End

Re: [COOT] MDO Unnatural modified Amino acid

Hi Kelvin, the 'group' in the monomer library do not necessarily correspond to the 'type' in CCD. The reason was that stricter rules for peptides and other groups were applied to the library. For MDO, there are 2 links: MDO-pept and pept-MDO to deal with this in a polypeptide. Of course, you cou