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Author Topic: changes of pdb format (A -> DA, T-> DT etc)  (Read 4298 times)

Offline ghzheng

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changes of pdb format (A -> DA, T-> DT etc)
« on: August 03, 2007, 10:51:02 am »
Hi Xiangjun,

I found the pdb format was recently changed a little bit in the PDB. For example, in the DNA atom coordinate part, the bases used to be A, T, C, G, but now  they became DA, DT, DC, DG.

So now if we directly run 3DNA for current pdb files downloaded from pdb, it will clash. Can you take into account this change to your next release? Is it OK that if I just change baselist.dat file to add in DA, DT, DC, DG?

Thanks.

Offline xiangjun

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« Reply #1 on: August 04, 2007, 09:39:48 am »
Hi,

Thanks for reporting the DNA residue name changes in the PDB. However, it would have been more helpful if you provide a concrete example, e.g., by giving the NDB or PDB id of an entry with such new names. Is this change only in NDB or PDB or both? Any link to the documentation for the changes?

What does you mean exactly "So now if we directly run 3DNA for current pdb files downloaded from pdb, it will clash"? Please provide a reproducible example step-by-step to show what error message you get.

Without knowing the details, I would guess that the issue is related to "unknown bases" to 3DNA, which was solved from the very beginning. Have you read the FAQ #7?

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline ghzheng

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« Reply #2 on: August 06, 2007, 12:57:48 pm »
Hi,

Sorry to confuse you. In fact, in PDB, all structures containing DNA polymers, use the new base names. But so far, NDB files still keep using the old format.

For example, check out and compare the part of DNA atoms in following two files:

1) PDB:   http://www.rcsb.org/pdb/files/1kx5.pdb
2) NDB:  ftp://ndbserver.rutgers.edu/NDB/coordin ... /1kx5.pdb1

But you are right, we can consider new names as "unknown bases".

Guohui

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.