On 26/05/10 16:01, Scott Classen wrote:
If I inspect the residue by looking at residue info I see that the atom names
now have * instead of ' and the phosphate oxygens are O1P O2P instead of OP1
OP2.
You are right of course, I'd forgotten how much Coot munges it into to
make it match
Well, I think I can make a guess.
Having been the target of a great deal of whingeing at the CCP4
developers meeting for hydrogen naming being in a mess (albeit not of
his making), Paul finally caved in and agreed to do the wrong thing and
kludge it in coot.
Unfortunately it is now broken
Failure to read for comprehension. Sorry, wrong problem, ignore me.
Kevin Cowtan wrote:
Well, I think I can make a guess.
Having been the target of a great deal of whingeing at the CCP4
developers meeting for hydrogen naming being in a mess (albeit not of
his making), Paul finally caved in
Hi Scott,
Congratulations for being up to date with you pre-release version.
AD, CD, GD and TD are the filenames that Refmac uses to hold restraints for Ad,
Cd, Gd and Td. The PDB standard names are DA, DC, DG and TD so it is not clear
to me what your custom cif files contain. Coot renames
Hi Paul,
here is one representative DNA base from my input PDB:
HETATM 2795 PDT D 3 35.132 -34.748 -8.254 1.00 72.83 P
HETATM 2796 OP1 DT D 3 34.082 -34.846 -9.292 1.00 80.59 O
HETATM 2797 OP2 DT D 3 35.991 -33.545 -8.152 1.00 69.11
Hi all,
My work flow is between coot and phenix.refine using only PDB version 3 DNA
atom/res names.
Currently my temporary work around is to do a global substitution using vi.
Assuming your DNA is chain D then the following 2 lines entered at the command
line will update the dna_from_coot.pdb
