Messages

1

General discussions (Q&As) / Re: Calculating the helical axis of DNA

« on: May 10, 2016, 05:53:59 am »

Hi again,
I have a further question to this thread...
If I'm analysing a multi-model PDB, I followed this steps:

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find_pair out.pdb out.inp
x3dna_ensemble extract -p hx_vec -o helix.out
This gives me the local helical axis. Is there a keyword (or an alternative procedure) to get the global linear helical axis for all the PDB models?
Thanks again!
Ramon

2

General discussions (Q&As) / Re: Calculating the helical axis of DNA

« on: May 09, 2016, 09:49:37 am »

Hi Xiang-Jun,
Thanks a lot for your explanation!!
Best,
Ramon

3

General discussions (Q&As) / Calculating the helical axis of DNA

« on: May 06, 2016, 06:15:55 am »

Dear all,
I would like to extract the DNA helical axis from a pdb, which contains a protein and DNA.
I first run

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find_pairs mypdb.pdb sample.inpThen, I guess I should run analyze (am I correct?):

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analyze sample.inpEven though I get the following error message some files are generated.

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......Processing structure #1: <sample.inp>......
[i] missing ' P  ' atom : residue name 'DA5', chain D, number [   1 ]
[i] missing ' OP1' atom : residue name 'DA5', chain D, number [   1 ]
[i] missing ' OP2' atom : residue name 'DA5', chain D, number [   1 ]
[i] missing ' P  ' atom : residue name 'DC5', chain E, number [   1 ]
[i] missing ' OP1' atom : residue name 'DC5', chain E, number [   1 ]
[i] missing ' OP2' atom : residue name 'DC5', chain E, number [   1 ]
[i] missing ' P  ' atom : residue name 'DA5', chain D, number [   1 ]
[i] missing ' P  ' atom : residue name 'DC5', chain E, number [   1 ]
My question is very simple. Where can I find the global linear helical axis in terms of its x, y, z coordinates?
At the end of the out file I see "local helical axis vector" where there is a vector for each pair. Should I average these vectors? I thought the axis was calculated by a fit to all base pairs, and so that there would be a single axis vector, not one for each base pair. Did I get something wrong?
Thanks in advance!
Ramon