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 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 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 PTd 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
