3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: maryatx3dna on March 13, 2014, 03:18:42 am

Title: std_base
Post by: maryatx3dna on March 13, 2014, 03:18:42 am: Sir,
I tried the std_base -fit option with xdna as in a earlier post. I tried the same with another modification. It works for A and G but not with C and T modification. I am attaching herewith C modification. I tried changing n2 to n1 ; but doesnt work. Please look through what goes wrong.

Thanking you
Title: Re: std_base
Post by: xiangjun on March 13, 2014, 01:20:45 pm: As shown in the attached image, the modified W is far off from a normal C. There is no N1 atom. Changing N2 to N1 does not help because N2 in W is connected to C4 and C6, not C2 and C6 as is the norm for N1 in pyrimidines. Thus, up to 3DNA v2.1 released on 2013jul10, W is not recognized a nucleotide, as can be verified by the following command:
Code: [Select]
find_pair -s W.pdb stdout W.pdb W.outs 1 # single helix 0 # number of bases 1 1 # explicit bp numbering/hetero atoms
So the reported behavior is as expected in the current 3DNA distributions. I will check if it is feasible to refine 3DNA's definition to include such modified cases in future releases. Alternatively, you may want to try the NUPARM/NUCGEN programs from the Bansal lab.

Xiang-Jun
Title: Re: std_base
Post by: maryatx3dna on March 14, 2014, 12:36:27 am: Sir,
So it means i couldnt get analysis of a modified DNA containing such a residue? No trick is possible?
Also
I didnt get NUCPARM . Is it available.? Could nucgen and nucparm can be used to analyze modified residues?

Thanking you for your valuable suggestions,

mary
Title: Re: std_base
Post by: xiangjun on March 14, 2014, 12:55:22 am: Quote
No trick is possible?
You could try changing C5Y to N1, then std_base would work. Just be careful with calculated parameters.

Quote
I didnt get NUCPARM . Is it available.? Could nucgen and nucparm can be used to analyze modified residues?
Just google NUPARM, you will find more information.

HTH,

Xiang-Jun
Title: Re: std_base
Post by: maryatx3dna on March 14, 2014, 07:18:55 am: Sir,
Thank you very much.
I think that's working.
Hope the overall structural parameters would not be affected by this change in atom. The analysis will not be completed without helical parameter; after all other analysis done.

Thank you very much

mary