Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.
Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.
In the last example, I created a series of regions with gradually increasing/decreasing scale in order to avoid large changes in scale over short distances.
To automate scale smoothing, each zoom block supports a smooth_distance and smooth_steps parameters. When using the smoothing feature, you define the zoom setting for your region of interest and then the number of smoothing steps and distance over which the scale smoothing is applied. Flanks around your zoomed region will have their scale progressively grow/shrink from the scale of your zoomed region to 1.
<zoom> chr = hs1 start = 120u end = 125u scale = 10 smooth_distance = 2r smooth_steps = 10 </zoom>
In this block, I define a 5Mb region on chromosome 1 that is expanded to 10x scale. The smoothing distance is 2r = 10Mb (here the "r" is relative to the size of the zoomed region) and smoothing is applied over 10 steps. Each smoothing step is 10Mb/10 = 1Mb and the scale decreases linearly across the smoothing regions.
You can define the smooth_distance parameter in relative units (r), chromosome units (u) or bases (b).