create bases?

[Charu]

Hi,
I am working on 3DFV from pdb. In Y chain of the DNA it has TTCAGATA... while in its complementary chain it has TATCTG , now I want two AA at the end of Z chain so that base pairs are completely formed, could you tell me if it's possible?
Thanks a lot!

[Charu]

The output file generated by analyze shows only 18 base pairs and does not include the first two TT in Y chain.

[xiangjun]

The output file generated by analyze shows only 18 base pairs and does not include the first two TT in Y chain.

The first two TTs on chain Y are not paired to AAs in 3dfv: 'find_pair' identifies all 18 bps available and 'analyze' outputs only parameters for those 18 bps. Everything is as expected.

As for your first question, i.e., pairing the two TTs in chain Y with two AAs in chain Z, have you checked if the two ends are pseudo-continuous in crystal packing? If so, write the full coordinates in a PDB file, and then 3DNA 'find_pair/analyze' will work accordingly. If not, you need to model the pairing with certain assumption/approximations. 3DNA has no direct facility for the job, but may be tailored for the purpose. On the other hand, please have a check of Coot, NAB, PyMol etc tools which may fit the job better. Please report back how it goes, and I will consider adapting 3DNA for your requirement if no other practical approach is available.

Xiang-Jun

[Charu]

Thanks a lot, sir.
I'm not very familiar with pdbs and PyMOL as I am still learning, I will definitely try to do as you guide in some time and let you know how it went.