Just to reiterate When coot (0.6.2-pre-1 Miramar (revision 2965) ) imports a DNA with PDB v3 atom/residue names it converts them to v2 atom/residue names... except for the C7 of Thymidine which remains C7 instead of being renamed C5M. Cheers, Scott
On May 26, 2010, at 8:01 AM, Scott Classen wrote: > Hi Paul, > > here is one representative DNA base from my input PDB: > > HETATM 2795 P DT 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 O > HETATM 2798 O5' DT D 3 34.440 -34.961 -6.827 1.00 73.70 O > HETATM 2799 C5' DT D 3 33.523 -36.031 -6.683 1.00 66.16 C > HETATM 2800 C4' DT D 3 33.012 -36.178 -5.257 1.00 60.11 C > HETATM 2801 O4' DT D 3 34.023 -36.716 -4.374 1.00 60.33 O > HETATM 2802 C3' DT D 3 32.463 -34.922 -4.587 1.00 59.89 C > HETATM 2803 O3' DT D 3 31.064 -35.096 -4.608 1.00 58.99 O > HETATM 2804 C2' DT D 3 33.001 -34.977 -3.156 1.00 60.10 C > HETATM 2805 C1' DT D 3 33.652 -36.352 -3.066 1.00 61.60 C > HETATM 2806 N1 DT D 3 34.891 -36.374 -2.271 1.00 63.31 N > HETATM 2807 C2 DT D 3 34.908 -37.067 -1.086 1.00 62.46 C > HETATM 2808 N3 DT D 3 36.105 -37.034 -0.423 1.00 65.81 N > HETATM 2809 C4 DT D 3 37.259 -36.396 -0.825 1.00 69.93 C > HETATM 2810 C5 DT D 3 37.168 -35.687 -2.084 1.00 67.04 C > HETATM 2811 C6 DT D 3 36.003 -35.711 -2.741 1.00 64.52 C > HETATM 2812 O2 DT D 3 33.940 -37.659 -0.647 1.00 63.45 O > HETATM 2813 O4 DT D 3 38.280 -36.444 -0.147 1.00 72.00 O > HETATM 2814 C7 DT D 3 38.347 -34.949 -2.642 1.00 65.55 C > > > 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. Oddly C7 remains C7? (which I believe is C5M or somesuch in the version > 2 atom names) > > When I save the coordinates from coot they look like this: > > > HETATM 2795 P Td D 3 35.132 -34.748 -8.254 1.00 72.83 > P > HETATM 2796 O1P Td D 3 34.082 -34.846 -9.292 1.00 80.59 > O > HETATM 2797 O2P Td D 3 35.991 -33.545 -8.152 1.00 69.11 > O > HETATM 2798 O5* Td D 3 34.440 -34.961 -6.827 1.00 73.70 > O > HETATM 2799 C5* Td D 3 33.523 -36.031 -6.683 1.00 66.16 > C > HETATM 2800 C4* Td D 3 33.012 -36.178 -5.257 1.00 60.11 > C > HETATM 2801 O4* Td D 3 34.023 -36.716 -4.374 1.00 60.33 > O > HETATM 2802 C3* Td D 3 32.463 -34.922 -4.587 1.00 59.89 > C > HETATM 2803 O3* Td D 3 31.064 -35.096 -4.608 1.00 58.99 > O > HETATM 2804 C2* Td D 3 33.001 -34.977 -3.156 1.00 60.10 > C > HETATM 2805 C1* Td D 3 33.652 -36.352 -3.066 1.00 61.60 > C > HETATM 2806 N1 Td D 3 34.891 -36.374 -2.271 1.00 63.31 > N > HETATM 2807 C2 Td D 3 34.908 -37.067 -1.086 1.00 62.46 > C > HETATM 2808 N3 Td D 3 36.105 -37.034 -0.423 1.00 65.81 > N > HETATM 2809 C4 Td D 3 37.259 -36.396 -0.825 1.00 69.93 > C > HETATM 2810 C5 Td D 3 37.168 -35.687 -2.084 1.00 67.04 > C > HETATM 2811 C6 Td D 3 36.003 -35.711 -2.741 1.00 64.52 > C > HETATM 2812 O2 Td D 3 33.940 -37.659 -0.647 1.00 63.45 > O > HETATM 2813 O4 Td D 3 38.280 -36.444 -0.147 1.00 72.00 > O > HETATM 2814 C7 Td D 3 38.347 -34.949 -2.642 1.00 65.55 > C > > I can send the custom cif file if you'd like. Essentially I've just updated > the atom names and * to ' etc for the mon_lib_list.cif, AD.cif, CD.cif, > GD.cif, and TD.cif files. > > Thanks, > Scott > > On May 26, 2010, at 2:46 AM, Paul Emsley wrote: > >> 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 residue >> name to match the dictionary. I'd be very surprised indeed if Coot changed >> the atom names (as you said it did). The Right Way, it seems to me, to fix >> this, is to "on-the-fly" change the dictionary identifiers to the PDB >> standard (this is what I believe Phenix does). This update is tentatively >> scheduled for 0.8. >> >> For the moment though, for handling cif/dictionary/atom-naming convention >> problems with Coot, I recommend the remediator. >> >> If Coot is really renaming the atoms (other than the coventional hydrogen >> name de-mangling), I'd like to know about it of course. >> >> Paul. >> >> >> ________________________________________ >> From: Scott Classen [sclas...@lbl.gov] >> Sent: 25 May 2010 19:16 >> To: Paul Emsley; William Scott >> Cc: COOT@JISCMAIL.AC.UK >> Subject: mon_lib_list.cif? >> >> Hi all, >> >> I just updated to 0.6.2-pre-1 (build 2965) via fink >> I am using the PDB v3 atom names for DNA so I copied over my custom cif >> files to replace: >> >> /sw/share/coot/lib/data/monomers/list/mon_lib_list.cif >> /sw/share/coot/lib/data/monomers/a/AD.cif >> /sw/share/coot/lib/data/monomers/c/CD.cif >> /sw/share/coot/lib/data/monomers/g/GD.cif >> /sw/share/coot/lib/data/monomers/t/TD.cif >> >> coot fires up OK. no complaints about the cif files, but coot is renaming my >> DNA atoms to version 2 atom names when it reads the PDB in.
