Do you have unidealities in your helix (things that are actually being penalized by an ideality score on some of the residues?).
If so, that could explain why your helix is not perfectly straight. Those are not straightened by Idealize SS - you have to run normal Idealize in order to resolve them. Idealize SS just sets the phi/psi/omega to their helix conformational values, while Idealize sets the peptide bond degrees of freedom.
jflat06,
I uploaded a solution for scientists named "Idealise SS test", which is what most of my testing was done on. I would hope that the ideality of the protein overall is decent. I use scripts "Idealize" and "MicroIdealize" (with various length settings) by spvincent at all wiggle power throughout all the folding stages.<p>
spvincent also wrote "ShowWorst" which can print up to 20 of the segments with worst ideality (and various other properties). The average for the 20 segments with the worst ideality is -1.605:<p>
Worst Ideality Ile 67 -4.45 Lys 66 -4.43 Lys 2 -2.247 Pro 1 -2.001 Lys 13 -1.944 Gln 75 -1.891 Ile 12 -1.712 Arg 43 -1.324 Glu 44 -1.239 Lys 64 -1.121 Lys 7 -1.119 Glu 65 -1.099 Lys 50 -0.999 Lys 10 -0.966 Ile 46 -0.952 Arg 6 -0.948 Lys 71 -0.939 Ile 53 -0.919 Lys 54 -0.896 Glu 70 -0.895
The average ideality for the worst 20 segments at the start is -0.756:
Worst Ideality Ile 67 -4.45 Lys 66 -4.43 Lys 2 -2.247 Pro 1 -2.001 Lys 13 -1.944 Gln 75 -1.891 Ile 12 -1.712 Arg 43 -1.324 Glu 44 -1.239 Lys 64 -1.121 Lys 7 -1.119 Glu 65 -1.099 Lys 50 -0.999 Lys 10 -0.966 Ile 46 -0.952 Arg 6 -0.948 Lys 71 -0.939 Ile 53 -0.919 Lys 54 -0.896 Glu 70 -0.895
BTW, a copy text button for the Recipe Output window would be nice--I found the file that contains it and copy/pasted but this would be much easier (especially for newbies) with a button.
jflat06,
Sorry the paste buffer for the start data evidently didn't take. Here it is:<p>
Worst Ideality Ile 75 -2.014 Ile 2 -0.832 Ile 9 -0.689 Ile 6 -0.685 Ile 7 -0.683 Ile 13 -0.683 Ile 73 -0.682 Ile 74 -0.682 Ile 10 -0.682 Ile 8 -0.682 Ile 18 -0.681 Ile 26 -0.68 Ile 27 -0.68 Ile 5 -0.68 Ile 45 -0.68 Ile 40 -0.68 Ile 14 -0.68 Ile 31 -0.68 Ile 25 -0.679 Ile 38 -0.678
My helixes do like to bend over and kink a lot…
jflat06,
When I first saw the "Idealize SS" tool, I thought that its purpose was to fully idealize each and every segment of the chosen SS–as opposed to being a SS painter/template. Serves me right for not reading the blog about it immediately and making assumptions. I know that naming tools is not always an easy task.<p>
Unfortunately, determining which segments need to be idealized first (or manually using Idealize on every segment), before using the Idealize SS tool is not easy task for beginners or non-coders.<p>
The idealize scripts written by spvincent are NC staples for me, but apparently they aren't idealizing to the degree necessary for the "Idealize SS" tool to create perfectly straight helices under all circumstances.
Right - If you take your solution and run Idealize AND Idealize SS on it, it will be perfectly straight (I just tried it). Idealize and Idealize SS do two different things, and both of them can keep a helix from being perfectly straight. Idealize SS sets phi/psi/omega, while Idealize sets the peptide bond DOFs.