A little background on the -negx option and rebuild of ssRNA

[mauricio esguerra]

Dear Dr. Lu,

As you are aware I have been using 3DNA for a while to exclusively analyse RNA structures as in our methods paper.
Right now I am just playing around and reconstructing the ribosome di-nucleotide steps after performing a single stranded analysis of 1jj2.pdb.
Basically what I do is:

1) Get step-parameters.
2) Script to rebuild from rows of step-parameter data (shift, slide, rise, tilt, roll, twist) a separate pdb file for each row/step.

When 3DNA finds a negative twist it reverses the direction of the x- and z-axes.
I would like to ignore this for all cases since I don't have Z-RNA conformations.
Is there another way besides using the -negx command?
Also, I might be missing out the deeper reason for the default behaviour of reversing the axes directions, I understand the reasons for base-pairs as you explain in your NAR paper of 2003 (page 5109), but I don't understand fully the reasons for the step case. Could you please expand a little bit more on this explanation, or point me to some of your papers which I might have overlooked?

Once more, thanks for your always excellent feedback, and for bearing with the newbies in the field like me.

Sincerely,

Mauricio Esguerra

[xiangjun]

Hi Mauricio,

You have touched a subtle point, indeed you are the first to post a question on the -negx option of "rebuild". I do not have time to go into details (due to a couple of deadlines), but here are my quick answers to your questions.

When 3DNA finds a negative twist it reverses the direction of the x- and z-axes.
I would like to ignore this for all cases since I don't have Z-RNA conformations.
Is there another way besides using the -negx command?

The -negx is designed for that specific purpose.

Also, I might be missing out the deeper reason for the default behaviour of reversing the axes directions, I understand the reasons for base-pairs as you explain in your NAR paper of 2003 (page 5109), but I don't understand fully the reasons for the step case. Could you please expand a little bit more on this explanation, or point me to some of your papers which I might have overlooked?

Have a look of my SCHNAaP/SCHNArP papers (J Mol Biol. 1997 Oct 31;273(3):668-80; J Mol Biol. 1997 Oct 31;273(3):681-91), where the "a" and "r" are the origins of the "analyze" and "rebuild" programs in 3DNA (both algorithm-wise and in code base).

HTH,

Xiang-Jun