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 [[log in to unmask]]
>> Sent: 25 May 2010 19:16
>> To: Paul Emsley; William Scott
>> Cc: [log in to unmask]
>> 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.