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Messages - Charu

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1
General discussions (Q&As) / Re: Analysis_assumptions!
« on: August 02, 2012, 04:20:38 am »
Thank you so much.

2
General discussions (Q&As) / Analysis_assumptions!
« on: July 24, 2012, 10:14:13 am »
Hi,

I am doing structure analysis for 3DFV which is GATA3-DNA complex structure. I wanted to ask that the assumption that mutating the bases using mutate_bases will show us the structural and binding differences that the protein GATA3 might have with respect to bases, is it correct?

because as i've been analysing, i've found almost all the same bonds and very little change in binding preferences of bases and bond lengths. I'm analysing using PyMOL.

Thanks.

3
General discussions (Q&As) / mutate_bases error
« on: July 24, 2012, 10:04:16 am »
Hi as I try to mutate bases in 3DFV using the command mutate_bases 'c=Y, s=14, m=DC' 3DFV.pdb 3DFV_mut.pdb, it shows a message:
"Out of 3 qualified entries

Y: 214783647_: [@@@] ===> [@@@.@] identical residue for mutation
@:..14_: [@@@] ===> identical residue for mutation
@:214783647_: [@@@] ===> [DC.@] required chainID/resnm/mutation not specified"

But I had mutated bases earlier using the same command. Could you please help me out?

4
General discussions (Q&As) / Re: create bases?
« 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.

5
General discussions (Q&As) / Re: create bases?
« 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.

6
General discussions (Q&As) / create bases?
« 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!

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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.