3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: Charu on July 12, 2012, 10:43:44 am

Title: create bases?
Post by: Charu on July 12, 2012, 10:43:44 am: 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!
Title: Re: create bases?
Post by: Charu on July 12, 2012, 11:10:36 am: The output file generated by analyze shows only 18 base pairs and does not include the first two TT in Y chain.
Title: Re: create bases?
Post by: xiangjun on July 12, 2012, 11:49:04 am: Quote
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 (http://www.rcsb.org/pdb/explore/explore.do?structureId=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
Title: Re: create bases?
Post by: Charu on July 24, 2012, 09:46:13 am: 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.