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Questions and answers => General discussions (Q&As) => Topic started by: maryatx3dna on September 04, 2014, 01:23:55 am

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Title: helical parameters
Post by: maryatx3dna on September 04, 2014, 01:23:55 am

Sir,

i would like to know which parameter should be changed to increase the width (C1'-C1'  or P-P) of the dna structure. is any helical parameter dependent on width of the double helix?
Title: Re: helical parameters
Post by: xiangjun on September 04, 2014, 10:43:20 am
What do you mean by the C1'-C1' width of DNA structure? Please be more specific with your question.

Xiang-Jun
Title: Re: helical parameters
Post by: maryatx3dna on September 11, 2014, 01:29:01 am
sir

i want a widened backbone,
C1'-C1' distance ~13 A

Also sir, how could i add custom P position in the Pxyz.dat file? could it help in getting a wide backbone.
Also i dont understand the usage of idx option.
Title: Re: helical parameters
Post by: xiangjun on September 11, 2014, 11:53:41 am
Quote
i want a widened backbone,
C1'-C1' distance ~13 A
From a pure geometric point of view, you may increase stretch. But then, H-bonds may disappear (with long distance), assuming you are talking about Watson-Crick pairs.

Quote
Also sir, how could i add custom P position in the Pxyz.dat file? could it help in getting a wide backbone.
Also i dont understand the usage of idx option.
Again, please be specific. What do you want to achieve? What have you tried? In posting questions, it always helps to provide some background information, and show your problems with concrete examples.

HTH,

Xiang-Jun
Title: Re: helical parameters
Post by: maryatx3dna on September 16, 2014, 01:35:55 am
Sir,

i have a modified nucleic acid with C1'-C1' distance about 13 A. i tried to create its rna counter part by using rebuild and std_base like that. but backbone didnt build up. so i added it using another software, minimized and got backbone linkages (O3'-P) correctly but puckering conformations are not good. so i thought if i could change P position information or i could change a normal rna into larger diameter i could get what i am looking for.
Title: Re: helical parameters
Post by: maryatx3dna on September 16, 2014, 05:45:36 am
ok sir, i got the backbone widened. it may suit my requiste

thank you sir
Title: Re: helical parameters
Post by: xiangjun on September 16, 2014, 12:35:27 pm
Quote
i got the backbone widened. it may suit my requiste
Glad to see you've been able to wide the backbone to ~ 13 A. For the benefit of other viewers of this thread, could you elaborate on how you did it?

In your previous message, you provided the following background info:
Quote
i have a modified nucleic acid with C1'-C1' distance about 13 A. i tried to create its rna counter part by using rebuild and std_base like that. but backbone didnt build up.
This is very informative. If you had supplied a sample PDB file of the modified nucleic acid you want to convert to its RNA counterpart, there could exist an alternative solution.

Xiang-Jun
Title: Re: helical parameters
Post by: maryatx3dna on September 17, 2014, 02:54:45 am
sir,

i got it by increasing the stretch as you have suggested.

thank you very much sir

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Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University